Methods and kits for treating cardiovascular disease

ABSTRACT

The present invention relates to methods and kits for treating cardiovascular disease.

RELATED APPLICATIONS

This application is a national stage application, filed under 35. U.S.C.§ 371, of International Application No. PCT/EP2018/050795, filed Jan.12, 2018, which claims priority to and benefit of U.S. ProvisionalApplication No. 62/445,395, filed on Jan. 12, 2017, and is acontinuation of U.S. application Ser. No. 15/649,175, filed on Jul. 13,2017, and U.S. application Ser. No. 15/649,177 filed on Jul. 13, 2017,the contents of each of which are incorporated herein in their entirety.

BACKGROUND OF THE INVENTION

Cardiovascular disease (CVD) is the leading cause of death globally.Each year in the U.S. there are 550,000 newly diagnosed CVD and thereare 200,000 recurrent CVD events each year.

Currently, a primary method for treating or preventing CVD is use ofstatins to lower levels of cholesterol, more specifically low-densitylipoprotein cholesterol (LDL-C). However, in 20% to 30% of CVD patients,statins are ineffective in preventing recurrent CV events. In a MayoClinic study and an unpublished recent European study, CVD patientstreated with statins had a 6 to 20% second event rate within two years,even though these subjects experienced lowered LDL-C cholesterol levelsfollowing treatment with statins.

In the “Jupiter study” (Ridker P M, Danielson E, Fonseca F A H, GenestJ, Gottto A M, Kastelein J J P, Koenig W, Libby P, Lorenzatti A J,MacFadyen J G, Nordestgaard B G, Shepherd J, Willerson J T, Glynn R Jfor the JUPITER Study Group. Rosuvastatin to prevent vascular events inmen and women with elevated C-reactive protein. N Engl J Med. 2008;359:2195-2207), subjects with elevated C-reactive protein (CRP) yet withlow cholesterol levels were treated with high doses of the statinCrestor to determine whether the treatment reduced CRP and reduced firstCVD events.

However, there exist subsets of CVD patients who respond (e.g., bylowering LDL-C cholesterol levels) to standard pharmacologicaltreatments, yet remain susceptible to first or second recurrent CVDevents. For example, in the JUPITER Study, of subjects treated withpotent statin therapy, Lp(a) was a significant determinant of remainingrisk for a first CVD event in spite of reduced LDL-C.

Accordingly, an unmet need exists for methods and kits to identifywhether an individual who may be susceptible to recurrent CVDevents—even with a standard pharmacological treatment—so that s/he canreceive increased monitoring and/or be provided a more aggressive andoptimal therapeutic intervention.

SUMMARY OF THE INVENTION

The present invention is based upon the discovery that specific IL-1genotype patterns stratify individuals into groups relating to theirmember's likelihood of over-producing IL-1 and having anauto-inflammatory response in the vascular wall in response to one ormore clinical indicators, including but not limited to Lp(a) levels,OxPL levels, triglyceride-rich lipoprotein levels, LDL-C levels, CRPlevels, and hypertension.

The present invention, comprising an IL-1 genetic test in combinationwith Lp(a), for example, predicts approximately 60% of recurrent cardiacevents and first events in individuals with Lp(a) and IL-1 genotypepatterns that are pro-inflammatory. The present invention enablescardiologists to increase monitoring of and/or provide more aggressive,optimal treatments or preventative regimens to specific subsets ofpatients.

The invention provides a method of selecting a human subject with adiagnosis of, suspected of having, or at risk for cardiovasculardisease; obtaining an isolated nucleic acid from a biological samplefrom the human subject; detecting the single nucleotide polymorphism(SNP) alleles in the isolated nucleic acid for each of the rs16944polymorphic locus, the rs1143623 polymorphic locus, the rs4848306polymorphic locus, the rs17561 polymorphic locus, and the rs1143634polymorphic locus; determining the human subject's IL-1 pattern based onthe detecting in step and the information disclosed in Table 1 and Table2; measuring the status of one or more clinical indicators in thebiological sample from the human subject, in another biological samplefrom the human subject, or in the human subject him/herself; andproviding a recommendation for a therapeutic or preventative regimenbased upon the human subject's IL-1 genotype pattern and measured statusof one or more clinical indicators.

In various aspects the invention provides methods for predicting therisk of and preventing a future cardiac event in a human subject byobtaining information regarding the human subject's single nucleotidepolymorphism (SNP) alleles for each of the rs16944 polymorphic locus,the rs1143623 polymorphic locus, the rs4848306 polymorphic locus, thers17561 polymorphic locus, and the rs1143634 polymorphic locus;determining whether the subject has a positive or negative IL-1 genotypepattern based on the information obtained and the information in Table 1and Table 2; determining the plasma concentration of LDL-C and/or Lp(a)in a plasma sample obtained from the subject; predicting the subject isat risk of a future cardiac event when the subject has a positive IL-1pattern and a total LDL-C plasma concentration of 70 mg/dL or lessand/or a total Lp(a) plasma concentration of at least 5 mg/dL; andadministering an IL-beta inhibitor to the subject. The IL-beta inhibitoris for example canakinumab. Optionally, the method further includesadministering one or more drugs from Table 4. The invention providesmethods for predicting the risk of and preventing a future cardiac eventin a human subject by obtaining information regarding the humansubject's single nucleotide polymorphism (SNP) alleles for each of thers16944 polymorphic locus, the rs1143623 polymorphic locus, thers4848306 polymorphic locus, the rs17561 polymorphic locus, and thers1143634 polymorphic locus; determining where the subject has apositive or negative IL-1 genotype pattern based on the informationobtained and the information disclosed in Table 1 and Table 2;determining the plasma concentration of LDL-C and/or Lp(a) in a plasmasample obtained from the subject; predicting the subject is at risk of afuture cardiac event when the subject has a positive IL-1 pattern and atotal LDL-C plasma concentration of at least 50 mg/dL and/or a totalLp(a) plasma concentration of at least 5 mg/dL; and administering aPCSK9 inhibitor or an antisense oligonucleotide that inhibitsapolipoprotein A-1 to the subject. The antisense oligonucleotide thatinhibits apolipoprotein A-1 is for example APO(a)Rx or ARC-LPA.Optionally, the method further includes comprising administering one ormore drugs from Table 3.

In other aspects, the invention provides methods for determining whethera human subject would receive a therapeutic benefit from/would beresponsive to IL-1 blocking drug and treating the subject by obtaininginformation regarding the human subject's single nucleotide polymorphism(SNP) alleles for each of the rs16944 polymorphic locus, the rs1143623polymorphic locus, the rs4848306 polymorphic locus, the rs17561polymorphic locus, and the rs1143634 polymorphic locus; determiningwhether the subject has a positive or negative IL-1 genotype patternbased on the information and the information in Table 1 and Table 2;determining the plasma concentration of LDL-C and/or Lp(a) in a plasmasample obtained from the subject determining the subject would receive atherapeutic benefit from/would be responsive to a IL-1 blocking drugwhen the subject has a positive IL-1 pattern and a total LDL-C plasmaconcentration of 70 mg/dL or less and/or a total Lp(a) plasmaconcentration of at least 5 mg/dL; and administering an IL-1 blockingdrug to the subject. The IL-1 blocking drug is for example canakinumab.Optionally, the method further includes administering one or more drugsfrom Table 4. In other aspects the invention provides methods fordetermining whether a human subject would receive a therapeutic benefitfrom/would be responsive to Lp(a) reducing drug and treating the subjectby obtaining information regarding the human subject's single nucleotidepolymorphism (SNP) alleles for each of the rs16944 polymorphic locus,the rs1143623 polymorphic locus, the rs4848306 polymorphic locus, thers17561 polymorphic locus, and the rs1143634 polymorphic locus;determining where the subject has a positive or negative IL-1 genotypepattern based on the information obtained and the information disclosedin Table 1 and Table 2; determining the plasma concentration of LDL-Cand/or Lp(a) in a plasma sample obtained from the subject; predictingthe subject is at risk of a future cardiac event when the subject has apositive IL-1 pattern and a total LDL-C plasma concentration of at least50 mg/dL and/or a total Lp(a) plasma concentration of at least 5 mg/dL;and administering a Lp(a) reducing drug to the subject. The Lp(a)reducing drug is a PCSK9 inhibitor or an antisense oligonucleotide thatinhibits apolipoprotein A-1. The antisense oligonucleotide that inhibitsapolipoprotein A-1 is for example, APO(a)Rx or ARC-LPA. Optionally, themethod further includes comprising administering one or more drugs fromTable 3.

For example, when a human subject has a positive IL-1 pattern based onthe information disclosed in Table 1 and Table 2 and has a measuredstatus of the one or more clinical indicators above a threshold levelfor the one or more clinical indicator, the human subject isadministered a treatment comprising at least one drug selected fromTable 3 to Table 7 or is administered a treatment comprising at leastone drug selected from Table 3 and at least one drug selected from Table4 to Table 7.

Alternatively, when the human subject has a positive IL-1 pattern basedon the information disclosed in Table 1 and Table 2 and has a measuredstatus of the one or more clinical indicators below a threshold levelfor the one or more clinical indicator, the human subject isadministered a treatment comprising at least one drug selected fromTable 3 and not comprising at least one drug selected from Table 4 toTable 7 or is administered a treatment not comprising at least one drugselected from Table 4 to Table 7.

When the clinical indicator is Lp(a) and the human subject has levels ofLp(a) above a threshold value, the at least one drug is selected fromTable 4 or the at least one drug is selected from Table 4 and furtherincludes at least one drug selected from Table 5. Alternatively, whenthe clinical indicator is LDL-C and the human subject has levels ofLDL-C above a threshold value, the at least one drug is selected fromTable 5 or the at least one drug is selected from Table 5 and furtherincludes at least one drug selected from Table 3. Additionally, when theclinical indicator is Triglyceride-rich lipoproteins and the humansubject has levels of Triglyceride-rich lipoproteins above a thresholdvalue, the at least one drug is selected from Table 6 or the at leastone drug is selected from Table 6 and further includes at least one drugselected from Table 3. When the clinical indicator is blood pressure andthe human subject has a blood pressure above a threshold value, the atleast one drug is selected from Table 7 or the at least one drug isselected from Table 7 and further includes at least one drug selectedfrom Table 3.

In another aspect the invention provides methods for treating a humansubject having or at risk for cardiovascular disease by (a) obtaininginformation regarding the human subject's single nucleotide polymorphism(SNP) alleles for each of the rs16944 polymorphic locus, the rs1143623polymorphic locus, the rs4848306 polymorphic locus, the rs17561polymorphic locus, and the rs1143634 polymorphic locus; (b) determiningeach human subject's IL-1 genotype pattern based on the informationobtained in step (a) and the information disclosed in Table 1 and Table2; (c) obtaining information regarding the human subject's status forone or more clinical indicators; and (d) administering a treatmentcomprising at least one drug selected from Table 4 to Table 7 oradministering a treatment comprising at least one drug selected fromTable 3 and at least one drug selected from Table 4 to Table 7 when thehuman subject has a positive IL-1 pattern based on the informationdisclosed in Table 1 and Table 2 and has a measured status of the one ormore clinical indicators above a threshold level for the one or moreclinical indicator, or administering a treatment comprising at least onedrug selected from Table 3 and not comprising at least one drug selectedfrom Table 4 to Table 7 or administering a treatment not comprising atleast one drug selected from Table 4 to Table 7 when the human subjecthas a positive IL-1 pattern based on the information disclosed in Table1 and Table 2 and has a measured status of the one or more clinicalindicators below a threshold level for the one or more clinicalindicator. When the clinical indicator is Lp(a) and the human subjecthas levels of Lp(a) above a threshold value, the at least one drug isselected from Table 4 or the at least one drug is selected from Table 4and further includes at least one drug selected from Table 3.Alternatively, when the clinical indicator is LDL-C and the humansubject has levels of LDL-C above a threshold value, the at least onedrug is selected from Table 5 or the at least one drug is selected fromTable 5 and further includes at least one drug selected from Table 3.When the clinical indicator is Triglyceride-rich lipoproteins and thehuman subject has levels of Triglyceride-rich lipoproteins above athreshold value, the at least one drug is selected from Table 6 or theat least one drug is selected from Table 6 and further includes at leastone drug selected from Table 3. Alternatively, when the clinicalindicator is blood pressure and the human subject has a blood pressureabove a threshold value, the at least one drug is selected from Table 7or the at least one drug is selected from Table 7 and further includesat least one drug selected from Table 3.

Also included in the invention are methods for determining whether ahuman subject is predisposed to having cardiovascular disease by (a)obtaining an isolated nucleic acid from a biological sample from thehuman subject; (b) detecting the single nucleotide polymorphism (SNP)alleles in the isolated nucleic acid for each of the rs16944 polymorphiclocus, the rs1143623 polymorphic locus, the rs4848306 polymorphic locus,the rs17561 polymorphic locus, and the rs1143634 polymorphic locus; (c)determining the human subject's IL-1 pattern based on the detecting instep (b) and the information disclosed in Table 1 and Table 2; and (d)measuring the status of one or more clinical indicators in thebiological sample from the human subject, in another biological samplefrom the human subject, or in the human subject him/herself. When thehuman subject has a positive IL-1 genotype pattern and has a measuredstatus of the one or more clinical indicators above a threshold levelfor the one or more clinical indicator, the subject is predisposed tohaving cardiovascular disease.

In another aspect the invention provides methods for determining whethera human subject having cardiovascular disease would receive atherapeutic benefit from/would be responsive to a drug selected fromTable 3 to Table 8, by (a) obtaining an isolated nucleic acid from abiological sample from the human subject; (b) detecting the singlenucleotide polymorphism (SNP) alleles in the isolated nucleic acid foreach of the rs16944 polymorphic locus, the rs1143623 polymorphic locus,the rs4848306 polymorphic locus, the rs17561 polymorphic locus, and thers1143634 polymorphic locus; (c) determining the human subject's IL-1pattern based on the detecting in step (c) and the information disclosedin Table 1 and Table 2; and (d) measuring the status of one or moreclinical indicators in the biological sample from the human subject, inanother biological sample from the human subject, or in the humansubject him/herself. When the human subject has a positive IL-1 genotypepattern and has a measured status of the one or more clinical indicatorsabove a threshold level for the one or more clinical indicator, thesubject would receive a therapeutic benefit from/would be responsive toa drug selected from Table 4 to Table 7. Alternatively, when the humansubject has a positive IL-1 genotype pattern and has a measured statusof the one or more clinical indicators below a threshold level for theone or more clinical indicator, the subject would not receive atherapeutic benefit from/would not be responsive to a drug selected fromTable 4 to Table 7. In various aspects the method further includesobtaining an isolated nucleic acid from a biological sample from thehuman subject; and detecting the single nucleotide polymorphism (SNP)alleles from the isolated nucleic acid for each of the rs16944polymorphic locus, the rs1143623 polymorphic locus, the rs4848306polymorphic locus, the rs17561 polymorphic locus, and the rs1143634polymorphic locus and/or measuring the status of one or more clinicalindicators in the biological sample from the human subject, in anotherbiological sample from the human subject, or in the human subjecthim/herself.

In yet another aspect the invention provides a kit including reagentsfor detecting the single nucleotide polymorphism (SNP) alleles in anisolated nucleic acid for each of the rs16944 polymorphic locus, thers1143623 polymorphic locus, the rs4848306 polymorphic locus, thers17561 polymorphic locus, and the rs1143634 polymorphic locus;optionally, reagents for measuring the status of one or more clinicalindicators; instructions for determining a human subject's IL-1 genotypepattern based on the detecting in step (a), and the informationdisclosed in Table 1 and Table 2; and instructions for determiningwhether a subject would receive a therapeutic benefit from/would beresponsive to at least one drug selected from Table 3 to Table 7 or atleast one drug selected from Table 3 and at least one drug selected fromTable 4 to Table 7.

As used herein, one or more clinical indicators include for example,Lp(a), Triglyceride-rich lipoproteins, OxPL, LDL-C, CRP, orhypertension.

Also contemplated by the invention are the use of drugs having a mode ofaction similar to or identical to a drug selected from Table 3 to Table7.

Any aspect or embodiment described herein can be combined with any otheraspect or embodiment as disclosed herein. While the disclosure has beendescribed in conjunction with the detailed description thereof, theforegoing description is intended to illustrate and not limit the scopeof the disclosure, which is defined by the scope of the appended claims.Other aspects, advantages, and modifications are within the scope of thefollowing claims.

The patent and scientific literature referred to herein establishes theknowledge that is available to those with skill in the art. All UnitedStates patents and published or unpublished United States patentapplications cited herein are incorporated by reference. All publishedforeign patents and patent applications cited herein are herebyincorporated by reference. All other published references, documents,manuscripts and scientific literature cited herein are herebyincorporated by reference.

Other features and advantages of the invention will be apparent from thefollowing detailed description and claim.

BRIEF DESCRIPTION OF THE DRAWINGS

The above and further features will be more clearly appreciated from thefollowing detailed description when taken in conjunction with theaccompanying drawings.

FIG. 1A-1B is a series of cartoons showing key events in cardiovasculardisease. FIG. 1A is a cartoon showing key players in atherosclerosis,which is an inflammatory disease. Reproduced from Ross“Atherosclerosis—An inflammatory disease” N Engl J Med (1999)340:115-126 and Libby “Current concepts of the pathogenesis of the acutecoronary syndromes” Circulation (2001) 140:365-372. FIG. 1B is aschematic cartoon showing how oxidized phospholipids activate vascularwall macrophages, which leads to release of pro-inflammatory cytokinesimplicated in clinical events.

FIG. 2 is a schematic showing how subjects with a specific IL-1 genotypepattern (i.e., “positive” IL-1 genotype pattern) overproduce IL-1β whenactivated whereas subjects with the opposite IL-1 genotype pattern(i.e., a “negative” IL-1 genotype pattern) does not overproduce IL-1βwhen activated. 30-60% of human subjects, depending on ethnic/racialbackground, carry IL-1 genotype patterns that over produce IL-1β.

FIG. 3 is a series of graphs showing the link between risk for secondCVD events and IL-1 genetic variants. FIG. 3, left panel, is a chartshowing that Lipoprotein(a) risk for second cardiovascular disease (CVD)events is conditional on IL-1 genetic variations. FIG. 3, right panel,is a chart showing that oxidized phospholipids on apolipoprotein B-100particles (OxPL/ApoB) risk for second CVD events is conditional on IL-1genetic variations.

FIG. 4 is a chart showing that Lipoprotein(a) risk for major adversecardiac events (MACE) is conditional on IL-1 genetic variations.

FIG. 5 is a plot showing Spearman correlations of logarithmic modifiedLp(a) and OxPL-apoB levels.

FIG. 6 is a series of graphs and their associated statistics showingmultivariable analysis derived odds ratios for CAD associated withLp(a), OxPL-apoB, or both among the traditional risk factors. Panel A,top, shows multivariable analysis derived odds ratios for CAD associatedwith Lp(a) among the traditional risk factors. CI=confidence interval,LDL-C=low-density lipoprotein (per increase of 25 mg/dl), hsCRP=highsensitivity C-reactive protein (per doubling), OxPL-apoB (per doubling),Lp(a) (per doubling), HDL-C=high-density lipoprotein (per increase of 10mg/dl), and triglycerides (per doubling). Panel B, middle, showsmultivariable analysis derived odds ratios for CAD associated withOxPL-apoB among the traditional risk factors. CI=confidence interval,LDL-C=low-density lipoprotein (per increase of 25 mg/dl), hsCRP=highsensitivity C-reactive protein (per doubling), OxPL-apoB (per doubling),Lp(a) (per doubling), HDL-C=high-density lipoprotein (per increase of 10mg/dl), and triglycerides (per doubling). Panel C, bottom showsmultivariable analysis derived odds ratios for CAD associated with bothLp(a) and OxPL-apoB among the traditional risk factors. CI=confidenceinterval, LDL-C=low-density lipoprotein (per increase of 25 mg/dl),hsCRP=high sensitivity C-reactive protein (per doubling), OxPL-apoB (perdoubling), Lp(a) (per doubling), HDL-C=high-density lipoprotein (perincrease of 10 mg/dl), and triglycerides (per doubling).

FIG. 7 is a plot showing cumulative event-free survival period over amedian of 43 months for clinical outcomes of CVD death, non-fatal MI,and stroke/TIA plotted according to medians of Lp(a) and IL-1 genotypeby Cox proportional hazard method.

DETAILED DESCRIPTION OF THE INVENTION

The present invention is based upon the discovery that specific IL-1genotype patterns stratify individuals into groups relating to theirmember's likelihood of over-producing IL-1 and having anauto-inflammatory response in the vascular wall in response to one ormore clinical indicator, including, but not limited to, Lp(a) levels,Triglyceride-rich lipoprotein levels, OxPL levels, LDL-C levels, CRPlevels, and hypertension. Importantly, it was discovered that even withoptimal LDL-C lowering, Lp (a) remains a risk factor to cardiovascularevent in subjects having an IL-1 positive genotype.

Traditional risk factors are important in identifying persons atincreased risk for cardiovascular disease (CVD) but do not fully explainglobal risk. For example, despite optimal secondary preventionstrategies, including achieving very low LDL-C levels, significantresidual CVD risk remains and most events are not prevented. Significantvariability also exists in the clinical expression of CVD among personswith similar risk factors. Finally, a sizable proportion of CVD risk maybe accounted for by low frequency but cumulative genetic variations thatare not fully described or understood.

Based on a preponderance of epidemiological and genetic studies, Lp(a),whose plasma levels are primarily genetically determined, is nowestablished as an independent, causal risk factor for CVD. Like otherrisk factors, Lp(a) has variable expression of CVD disease at differentcirculating level thresholds. Understanding the influences that modifythe strength of risk factors may allow more rational and personalizedtherapy for patients at risk for CVD.

The present invention provides in part, an IL-1 genetic test incombination with Lp(a), for example, that predicts approximately 60% ofrecurrent cardiac events within the first two years of an initial eventand intervention. The present invention enables cardiologists toincrease monitoring of and/or provide more aggressive and optimalpreventive interventions or treatments to specific subsets of patients.The IL-1 genetic test in combination with an clinical indicator hasfurther utility in predicting a cardiac event in an individual not knownto have previously had a cardiac event.

It has been discovered that individuals can be stratified into one oftwo IL-1 genotype patterns, i.e., Positive or Negative based upon theircomplex IL-1 genotype for three or five SNP loci. See, Table 1 and Table2.

TABLE 1 rs17561 + rs4848306 − rs1143623 − rs16944 − rs1143634 + IL-14845 3737 1464 511 3954 Pattern T/‡ †/† G/G C/C T/† Positive G/G †/† G/GC/C †/† Positive ‡/‡ †/† G/G C/C C/C Positive T/‡ C/† G/G C/T T/†Positive G/G C/† G/G C/T †/† Positive ‡/‡ C/† G/G C/T C/C Positive T/‡C/C C/G C/T T/† Positive G/G C/C C/G C/T †/† Positive ‡/‡ C/C C/G C/TC/C Positive T/‡ C/T C/G C/T T/† Negative G/G C/T C/G C/T †/† Negative‡/‡ C/T C/G C/T C/C Negative T/‡ C/C G/G T/T T/† Positive G/G C/C G/GT/T †/† Positive ‡/‡ C/C G/G T/T C/C Positive T/‡ C/C C/* T/T T/†Negative G/G C/C C/* T/T †/† Negative ‡/‡ C/C C/* T/T C/C Negative

TABLE 2 rs17561 + rs16944 − rs1143634 + 4845 511 3954 IL-1 Pattern T/‡C/C T/† Positive G/G C/C †/† Positive ‡/‡ C/C C/C Positive T/‡ C/T T/†Positive G/G C/T †/† Negative ‡/‡ C/T C/C Negative T/‡ T/T T/† NegativeG/G T/T †/† Negative ‡/‡ T/T C/C Negative

In Table 1 and Table 2, “*” is G or C; “†” is C or T; and “‡” is G or T.

A subject having an uncommon complex IL-1 genotype not exemplified inTable 1 and Table 2 is considered herein as having an IL-1 genotypepattern of “Negative”.

A subject may be stratified into an IL-1 genotype pattern by the SNPloci listed in Table 1 and Table 2 and/or SNP loci in linkagedisequilibrium (LD), e.g., 80% LD, with the SNP loci listed in Table 1and Table 2

A subject of certain racial/ethnic groups may be stratified into an IL-1genotype pattern based upon five SNP loci listed in Table 1; otherracial/ethnic groups may require three SNP loci (as in Table 2) to bestratified into an IL-1 genotype pattern. Differences in the frequenciesor even the absence of a specific SNP of specific SNPs in certainracial/ethnic groups may require the inclusion of additional informativeSNPs.

The present invention allows a diagnosis and optimal treatmentrecommendation for a subject based upon his/her IL-1 genotype patternand status of one or more clinical indicators.

Accordingly the invention includes a method for predicting the risk ofand preventing a future cardiac event in a human subject by obtaininginformation regarding the human subject's single nucleotide polymorphism(SNP) alleles for each of the rs16944 polymorphic locus, the rs1143623polymorphic locus, the rs4848306 polymorphic locus, the rs17561polymorphic locus, and the rs1143634 polymorphic locus. If the subjectis determined to have a positive or negative IL-1 genotype pattern(based on the information obtained and the information in Table 1 andTable 2 and has a total LDL-C plasma concentration of 70 mg/dL or lessand/or a total Lp(a) plasma concentration of at least 5 mg/dL thussubject is administered an IL-beta inhibitor. The IL-beta inhibitor isfor example canakinumab. Optionally, the method further includesadministering one or more drugs from Table 4. The subject is at risk ofa future cardiac event when the subject has a positive IL-1 pattern anda total LDL-C plasma concentration of at least 50 mg/dL and/or a totalLp(a) plasma concentration of at least 5 mg/dL. A future cardiac eventis prevented by administering a PCSK9 inhibitor or an antisenseoligonucleotide that inhibits apolipoprotein A-1 to the subject. Theantisense oligonucleotide that inhibits apolipoprotein A-1 is forexample APO(a)Rx or ARC-LPA. Optionally, the method further includescomprising administering one or more drugs from Table 3.

In other aspects the invention includes methods for determining whethera human subject would receive a therapeutic benefit from/would beresponsive to IL-1 blocking drug or to to Lp(a) reducing drug andtreating the subject by obtaining information regarding the humansubject's single nucleotide polymorphism (SNP) alleles for each of thers16944 polymorphic locus, the rs1143623 polymorphic locus, thers4848306 polymorphic locus, the rs17561 polymorphic locus, and thers1143634 polymorphic locus. If the subject has a positive IL-1 patternand a total LDL-C plasma concentration of 70 mg/dL or less and/or atotal Lp(a) plasma concentration of at least 5 mg/dL; thus subject isadministered an IL-1 blocking drug to the subject. The IL-1 blockingdrug is for example canakinumab. Optionally, the method further includesadministering one or more drugs from Table 4. The subject is predictedto be at risk of a future cardiac event when the subject has a positiveIL-1 pattern and a total LDL-C plasma concentration of at least 50 mg/dLand/or a total Lp(a) plasma concentration of at least 5 mg/d. Thesubject is treated by administering a Lp(a) reducing drug to thesubject. The Lp(a) reducing drug is a PCSK9 inhibitor or an antisenseoligonucleotide that inhibits apolipoprotein A-1. The antisenseoligonucleotide that inhibits apolipoprotein A-1 is for example,APO(a)Rx or ARC-LPA.

In a non-limiting example, if a subject has a Positive IL-1 genotypepattern and has a measured Lp(a) level (an exemplary clinical indicator)above a threshold value, the subject is administered an Lp(a) reducingdrug and, optionally, is administered an Lp(a) reducing drug and an IL-1lowering drug, but may also receive an IL-1 lowering drug without anLp(a) reducing drug; whereas a subject who has a Positive IL-1 genotypepattern and has a measured Lp(a) level below a threshold value is notadministered an Lp(a) reducing drug and, optionally, is administered anIL-1 lowering drug.

Similarly, if a subject has a Positive IL-1 genotype pattern and has ameasured LDL-C level above a threshold value, then the subject isadministered an LDL-C reducing drug, e.g., a statin, and, optionally, isadministered an LDL-C reducing drug and an IL-1 lowering drug, whereas asubject who has a Positive IL-1 genotype pattern and has a measuredLDL-C level below a threshold value is not administered an LDL-Creducing drug and, optionally, is administered an IL-1 lowering drug.

Additionally, when the clinical indicator is blood triglycerides, asubject who has a Positive IL-1 genotype pattern and high measuredtriglyceride levels above a threshold value, the subject is administereda triglyceride reducing drug and, optionally, is administered atriglyceride reducing drug and an IL-1 lowering drug, whereas a subjectwho has a Positive IL-1 genotype pattern and does not have high measuredtriglyceride levels is not administered a triglyceride reducing drugand, optionally, is administered an IL-1 lowering drug.

Moreover, when the clinical indicator is blood pressure, a subject whohas a Positive IL-1 genotype pattern and high blood pressure (above athreshold value), the subject is administered a blood pressure reducingdrug and, optionally, is administered a blood pressure reducing drug andan IL-1 lowering drug, whereas a subject who has a Positive IL-1genotype pattern and does not have high blood pressure is notadministered a blood pressure reducing drug and, optionally, isadministered an IL-1 lowering drug.

When the clinical indicator is CRP, a subject who has a Positive IL-1genotype pattern and high CRP levels (above a threshold value), thesubject is administered a CRP reducing drug and, optionally, isadministered a CRP reducing drug and an IL-1 lowering drug, whereas asubject who has a Positive IL-1 genotype pattern and does not have highCRP is not administered a CRP reducing drug and, optionally, isadministered an IL-1 lowering drug.

When the clinical indicator is OxPL levels, a subject who has a PositiveIL-1 genotype pattern and high OxPL levels (above a threshold value),the subject is administered a OxPL reducing drug and, optionally, isadministered a OxPL reducing drug and an IL-1 lowering drug, whereas asubject who has a Positive IL-1 genotype pattern and does not have highOxPL is not administered a OxPL reducing drug and, optionally, isadministered an IL-1 lowering drug.

Alternately, if a subject has a Positive IL-1 genotype pattern and morethan one measured clinical indicator at each marker's threshold, thesubject is administered a first drug that reduces levels of the firstclinical indicator and a second drug that reduces levels of the secondclinical indicator and, optionally, is administered the first drug thatreduces levels of the first clinical indicator, the second drug thatreduces levels of the second clinical indicator, and an IL-1 loweringdrug.

Levels of more than one clinical indicator may be reduced by a singledrug; in these cases, the subject with Positive IL-1 genotype patternand more than one measured clinical indicator at each marker's thresholdis administered the single drug that reduces levels of more than oneclinical indicator, and, optionally, is administered the single drugthat reduces levels of more than one clinical indicator and an IL-1lowering drug.

The threshold value for a clinical indicator depends on the particularclinical indicator measured. For example, the threshold value for Lp(a)may be 5 mg/dL or more, 10 mg/dL or more, 20 mg/dL or more, 30 mg/dL ormore, 50 mg/dL or more; 60 mg/dL or more, 70 mg/dL, 80 mg/dL or more, or90 mg/dL or more. The threshold value for Lp(a) may be 5 mg/dL or more.Alternatively, the threshold value for Lp(a) may be 5 mg/dL or less, 10mg/dL or less, 20 mg/dL or less, 30 mg/dL or more, 50 mg/dL or less; 60mg/dL or less, 70 mg/dL, 80 mg/dL or less, or 90 mg/dL or less.

The threshold value of LDL-C may be 25 mg/dL or more, 50 mg/dL or more,60 mg/dL or more, 70 mg/dL or more, 80 mg/dL or more, 90 mg/dL or more,100 mg/dL or more, 110 mg/dL or more, 120 mg/dL or more, 150 mg/dL ormore, 160 mg/dL or more, 170 mg/dL or more, 180 mg/dL or more, 190 mg/dLor more. Alternatively, the threshold value of LDL-C may be 25 mg/dL orless, 50 mg/dL or less, 60 mg/dL or less, 70 mg/dL or less, 80 mg/dL orless, 90 mg/dL or less

The threshold value for triglycerides may be 500 mg/dL or more, 400mg/dL or more, 300 mg/dL or more, 200 mg/dL or more; 190 mg/dL or more,180 mg/dL or more, 170 mg/dL or more, 160 mg/dL or more, 150 mg/dL ormore, 140 mg/dL or more, or 130 mg/dL or more. Alternatively, thethreshold value for triglycerides may be 500 mg/dL or less, 400 mg/dL orless, 300 mg/dL or less, 200 mg/dL or less; 190 mg/dL or less, 180 mg/dLor less, 170 mg/dL or less, 160 mg/dL or less, 150 mg/dL or less, 140mg/dL or less, or 130 mg/dL or less, 120 mg/dL or less, 110 mg/dL orless, 100 mg/dL or less, or 90 mg/dL or less.

The threshold value for high blood pressure may be 140/90 or more; or120/80 or more. Alternatively, the threshold value for high bloodpressure may be 140/90 or less; or 120/80 or less.

A threshold value for CRP may be 20 mg/L or more, 15 mg/L or more 10mg/L or more, 7.5 mg/L or more, 5 mg/L or more, or 2.5 mg/L or more.Alternatively, the CRP may be 20 mg/L or less, 15 mg/L or less, 10 mg/Lor less, 7.5 mg/L or less, 5 mg/L or less, or 2.5 mg/L or less.

The threshold value for a clinical indicator may vary for an individualbased upon other levels of other clinical indicators and/or other CVDrisk predictors, e.g., sex, age, height, weight, previous history of aheart attack and/or the presence of other metabolic disorders, e.g.,Type II diabetes. Thus, depending on the these, and other, factors, athreshold value for a clinical indicator may be reduced by 1%, 5%, 10%,20%, 30%, 40%, 50% or any percentage in between; alternately, dependingon the these, and other, factors, a threshold value for a clinicalindicator may be increased by 1%, 5%, 10%, 20%, 30%, 40%, 50% or anypercentage in between.

The present invention, in view of the disclosures of Table 1 and Table2, allows a skilled artisan to identify:

-   -   Subjects likely to derive more benefit from specific drug;    -   Subjects with one IL-1 genotype pattern who may respond        favorably to lower levels of the drug than subjects of a        different pattern;    -   Subjects who should be on an IL-1-blocking drug earlier than        others because their genotype pattern is more aggressive; and    -   Subjects with an IL-1 dominant disease subtype that may be        predictably responsive to IL-1-blocking drugs but not other        agents which have different modes of action.

Modulators of IL-1 biological activity (e.g., IL-1α, IL-1β, or IL-1receptor antagonist) or a protein encoded by a gene that is in linkagedisequilibrium with an IL-1 gene, can comprise any type of compound,including a protein, peptide, peptidomimetic, lipid, small molecule, ornucleic acid. A modulator may be a botanical or extract of a botanical.

A modulator may indirectly act upon an IL-1 gene in that the modulatoractivates or represses a gene or protein that, in turn or ultimately,acts upon the IL-1 gene. As used herein, the term “ultimately” is meantthat the modulator acts upon a first gene or protein and the first geneor protein directly acts upon the IL-1 gene or the first gene or proteinacts upon a second gene or protein which directly (or indirectly) actsupon the IL-1 gene. Such indirect gene regulation is well known in theart. A modulator that acts upstream to the IL-1 gene is useful in thepresent invention. An example of a modulator that acts upstream of theIL-1 gene is Aldeyra's NS2 compound which traps excess free aldehydes,which are known to activate a number of intracellular inflammatoryfactors including NF-kB, a prominent protein in the inflammatoryresponse. Another example of that acts upstream of the IL-1 gene isIonis Pharmaceutical's IONIS-APO(a)-L_(Rx) and Arrowhead's ARC-LPA,which reduces Lp(a) levels that would be expected to activate arterialwall macrophages to produce IL-1β.

Alternately, a modulator may act downstream of the IL-1 gene by directlyor indirectly affecting a gene or protein that operates in parallel toIL-1 in an inflammatory cascade.

An agonist can be a protein or derivative thereof having at least onebioactivity of the wild-type protein, e.g., receptor binding activity.An agonist can also be a compound that upregulates expression of a geneor which increases at least one bioactivity of a protein. An agonist canalso be a compound which increases the interaction of a polypeptide withanother molecule, e.g., a receptor.

An antagonist can be a compound which inhibits or decreases theinteraction between a protein and another molecule, e.g., blocking thebinding to receptor, blocking signal transduction, and preventingpost-translation processing (e.g., IL-1 converting enzyme (ICE)inhibitor). An antagonist can also be a compound that downregulatesexpression of a gene or which reduces the amount of a protein present.The antagonist can be a dominant negative form of a polypeptide, e.g., aform of a polypeptide which is capable of interacting with a target.Antagonists, include nucleic acids (e.g., single (antisense) or doublestranded (triplex) DNA or PNA and ribozymes), protein (e.g., antibodies)and small molecules that act to suppress or inhibit IL-1 transcriptionand/or protein activity.

An anti-inflammatory drug refers to any agent or therapeutic regimen(including a pharmaceutical, biologic, nutraceutical, and botanical)that prevents or postpones the development of or alleviates a symptom ofthe particular disease, disorder, or condition that involved aninflammatory process in the subject. The drug can be a polypeptide,peptidomimetic, nucleic acid or other inorganic or organic molecule, a“small molecule,” vitamin, mineral, or other nutrient. The drugmodulates the production of the active IL-1β or IL-11α polypeptides, orat least one activity of an IL-1 polypeptide, e.g., interaction with areceptor, by mimicking or potentiating (agonizing) or inhibiting(antagonizing) the effects of a naturally-occurring polypeptide. Ananti-inflammatory drug also includes, but is not limited to,anti-cholesterol drugs (e.g., statins), diabetes mellitus drugs, drugsthat treat acute syndromes of the heart and vascular system (e.g., acardiovascular disease), and arthritis.

Non-limiting examples of anti-inflammatory drugs that modulate IL-1biological activity useful in the present invention are listed in Table3. These drugs generally have a mode of action that includes modulationof IL-1 gene expression, modulation of inflammasomes, IL-1 receptorblocking agents, agents that bind IL-1β or IL-1α to inhibit attachmentto the active receptor. IL-1 blocking drugs may also indirectly targetIL-1 by blocking key activators of IL-1 gene expression.

TABLE 3 ABT-981 Gevokizumab AC-701 Givinostat Ammoniumtrichloro-tellurate Isunakinra Anakinra Rilonacept Anakinra BiosimilarRON-2315 APX-002 Sairei-To Binimetinib SER-140 Can-04 Tadekinig-alphaCanakinumab Xilonix Diacerein XL-130 DLX-2681 NUTRILITE ® IL1 HeartHealth Nutrigenomic Dietary Supplement

Twenty percent of the general population has elevated Lp(a), an LDL-likeparticle which may be more atherogenic than LDL cholesterol.Unfortunately, elevated Lp(a) levels do not generally respond to statindrugs or to diet modifications. Lp(a) levels are reduced by niacin inthose who can tolerate the side effects.

Non-limiting examples of Lp(a) reducing drugs useful in the presentinvention are listed in Table 4:

TABLE 4 PCSK9 inhibitor Repatha (Amgen) ARC-LPA (Arrowheas) PCSK9inhibitor Pralvent Alirocumab (Regeneron) APO(a)-L_(RX) (Ionis)

Non-limiting examples of anti-cholesterol drugs useful in the presentinvention are listed in Table 5:

TABLE 5 Advicor Pitavastatin (Livalo) alirocumab Lofibra lovastatin(Altoprev and Mevacor) niacin amlodipine-atorvastatin niacin-lovastatinAntara niacin-simvastatin atorvastatin Niacor Caduet Niaspancholestyramine Praluent Colestid Pravastatin (Pravachol) colestipolPrevalite rosuvastatin (Crestor) Questran Endur-Acin Light evolocumabQuestran ezetimibe Repatha SureClick ezetimibe-simvastatin RepathaSyringe fenofibrate Simcor fenofibric acid (choline) simvastatin (Zocor)fenofibric acid Slo-Niacin Fenoglide Tricor Fibricor Triglidefluvastatin Trilipix fluvastatin (Lescol and Lescol XL) Vytorinatorvastatin (Lipitor) Zetia Lipofen

Non-limiting examples of anti-Triglyceride-rich lipoproteins drugsuseful in the present invention are listed in Table 6:

TABLE 6 fibrates (fenofibrate and gemfibrozil) niacin omega-3 fattyacids Volanesorsen Alipogene tiparvovec (Glybera) Lomitapide

Non-limiting examples of blood pressure reducing drugs useful in thepresent invention are listed in Table 7:

TABLE 7 diuretics Altace Vasotec Prinivil Norvasc Diovan ProcardiaCozaar Tenormin Tiazac Tekturna Adalat CC Afeditab CR Cardizem LopressorCorgard Toprol-XL

Non-limiting examples of diabetes mellitus drugs include: acarbose,ActoplusMET, Actos, Amaryl, Avandamet, Avandia, bromocriptine, Bydureon,Byetta, Farxiga, Fortamet, glimepiride, glipizide, Glucophage,GlucophageXR, Glucovance, Glumetza, glyburide, Humalog, Invokana,Janumet, Januvia, Kombiglyze XR, Lantus, Lantus Solostar, Levemir,metformin, Novolog, NovologFlexpen, Novolog Mix70-30FlexPen, Onglyza,Parlodel, pioglitazone, Prandin, Starlix, Tradjenta, Victoza2-Pak, andWelChol.

Non-limiting examples of drugs that treat acute syndromes of the heartand vascular system include: Altace, Arixtra metoprolol tartrate,aspirin, atenolol, Bystolic, BRILINTA, carvedilol, clopidogrel, Coreg,Coumadin, diovan, enoxaparin, heparin, Lisinopril, Lopressor, Lovaza,Lovenox, metoprolol tartrate, Niaspan, Nitro-Bid, nitroglycerin, Plavix,Ramipril, and warfarin.

Any of the drugs listed in Table 3 to Table 7 (alone or together) may beused in the present invention. An individual may be administered one ormore drugs of Table 3 to Table 7 at a higher dose or at a lower dose(e.g., the dose of a single treatment and/or a daily dose comprising oneor more single treatments) depending on his/her IL-1 genotype patternand status of one or more clinical indicators; alternately, theindividual may be not given the particular drug depending on his/herIL-1 genotype pattern and status of one or more clinical indicators andinstead may be administered a different drug. For example, rather thanbeing administered Xilonix, which is a human monoclonal antibody againstIL-1α, based on the individual's IL-1 genotype pattern and clinicalindicator status, the individual may be administered Gevokizumab, whichis a human monoclonal antibody against IL-1β.

Additionally, drugs other than those listed in Table 3 to Table 7 may beused in the present invention. For this, an alternate drug having a modeof action (MOA) similar to or identical to a drug listed in Table 3 toTable 7 may be provided instead of or in addition to the drug listed inTable 3 to Table 7. One skilled in the art is able to determinealternate drugs that are useful in the present invention.

A subject may be administered one or more drugs from Table 3 to Table 7or one or more alternate drugs having a MOA similar to or identical to adrug listed in Table 3 to Table 7 at the standard therapeutic dose. Adrug may be given at a dose lower than the standard therapeutic dose,e.g., 99%, 95%, 90%, 85%, 80%, 75%, 70%, 60%, 50%, 40%, 30%, 20%, 15%,10%, or 5%, and any percentage in between lower than the standardtherapeutic dose. A drug may be given at a dose higher than the standardtherapeutic dose, e.g., 5%, 10%, 15%, 20%, 30%, 40%, 50%, 60%, 70%, 75%,80%, 85%, 90%, 95%, 100%, 125%, 150%, 175%, 200%, 300%, 400%, 500%,600%, 700%, 800%, 900%, 1000%, 2000%, or more, and any percentage inbetween higher than the standard therapeutic dose. For example, if astandard therapeutic dose is 10 mg per day, a subject may be given 7 mgper day as a lower than standard therapeutic dose or 13 mg per day as ahigher than standard therapeutic dose.

A subject in need of treatment for a CVD or at risk for CVD will provideor has provided a biological sample comprising a nucleic acid andcomprising at least one clinical indicator; alternately, when bloodpressure is the clinical indicator, the subject will provide or hasprovided a biological sample comprising a nucleic acid and has his/herblood pressure measured. Single nucleotide polymorphism (SNP) alleles inthe isolated nucleic acid for each of the, at least 3, or 5 polymorphicloci identified in Table 1 and Table 2, or polymorphic loci in linkagedisequilibrium to the polymorphic loci identified in Table 1 and Table 2will be detected by any method known in the art and a composite IL-1genotype will be determined. From the determined composite IL-1genotype, a Positive or Negative IL-1 genotype pattern will bedetermined based on the information disclosed in Table 1 and Table 2. Atleast one of the subject's clinical indicators will be measured. Whenthe subject has a Positive IL-1 genotype pattern and has a measuredclinical indicator above a threshold level, s/he will be administeredone or more drugs identified in Table 3 to Table 7, or alternately, beadministered one or more drugs identified in Table 3 to Table 7 and oneor more drug identified in Table 3. When the subject has a Positive IL-1genotype pattern and has a measured clinical indicator below a thresholdlevel, s/he will not be administered a drug identified in Table 4 toTable 7, or alternately, will be administered more drug identified inTable 3. The present invention further includes use of alternate drugsto the drugs listed in Table 3 to Table 7.

A drug may be useful in the present invention for more than one diseaseor disorder relevant to the present invention.

Any drug of Table 3 to Table 7 may be administered with any other drugor drugs of Table 3 to Table 7.

Any drug of Table 3 to Table 7 may be administered with any other drugor drugs known in the art that is capable of treating or reducing asymptom of one or more disease or disorder relevant to the presentinvention.

A drug is prepared depending in its route of drug administration.Examples of drug administration routes that are useful in the presentinvention are described on the U.S. Food and Drug Administration'swebsite at the World Wide Web(www.fda.gov/Drugs/DevelopmentApprovalProcess/FormsSubmissionRequirements/ElectronicSubmissions/DataStandardsManualmonographs/ucm071667.htm).

Preparations for oral administration generally contain inert excipientsin addition to the active pharmaceutical ingredient. Oral preparationsmay be enclosed in gelatin capsules or compressed into tablets. Commonexcipients used in such preparations include pharmaceutically compatiblefillers/diluents such as microcrystalline cellulose, hydroxypropylmethylcellulose, starch, lactose, sucrose, glucose, mannitol, sorbitol,dibasic calcium phosphate, or calcium carbonate; binding agents such asalginic acid, carboxymethylcellulose, microcrystalline cellulose,gelatin, gum tragacanth, or polyvinylpyrrolidone; disintegrating agentssuch as alginic acid, cellulose, starch, or polyvinylpyrrolidone;lubricants such as calcium stearate, magnesium stearate, talc, silica,or sodium stearyl fumarate; glidants such as colloidal silicon dioxide;sweetening agents such as sucrose or saccharin; flavoring agents such aspeppermint, methyl salicylate, or citrus flavoring; coloring agents; andpreservatives such as antioxidants (e.g., vitamin A, vitamin C, vitaminE, or retinyl palmitate), citric acid, or sodium citrate. Oralpreparations may also be administered as aqueous suspensions, elixirs,or syrups. For these, the active ingredient may be combined with varioussweetening or flavoring agents, coloring agents, and, if so desired,emulsifying and/or suspending agents, as well as diluents such as water,ethanol, glycerin, and combinations thereof.

For parenteral administration (including subcutaneous, intradermal,intravenous, intramuscular, and intraperitoneal), the preparation may bean aqueous or an oil-based solution. Aqueous solutions may include asterile diluent such as water, saline solution, a pharmaceuticallyacceptable polyol such as glycerol, propylene glycol, or other syntheticsolvents; an antibacterial and/or antifungal agent such as benzylalcohol, methyl paraben, chlorobutanol, phenol, thimerosal, and thelike; an antioxidant such as ascorbic acid or sodium bisulfite; achelating agent such as ethylenediaminetetraacetic acid (EDTA); a buffersuch as acetate, citrate, or phosphate; and/or an agent for theadjustment of tonicity such as sodium chloride, dextrose, or apolyalcohol such as mannitol or sorbitol. The pH of the aqueous solutionmay be adjusted with acids or bases such as hydrochloric acid or sodiumhydroxide. Oil-based solutions or suspensions may further comprisesesame, peanut, olive oil, or mineral oil.

For topical (e.g., transdermal or transmucosal) administration,penetrants appropriate to the barrier to be permeated are generallyincluded in the preparation. Transmucosal administration may beaccomplished through the use of nasal sprays, aerosol sprays, tablets,or suppositories, and transdermal administration may be via ointments,salves, gels, patches, or creams as generally known in the art. Topicalocular formulations, e.g., eye drops and eye ointments, are considered.

The amount of agent that is administered to the subject can and willvary depending upon the type of agent, the subject, and the particularmode of administration. Those skilled in the art will appreciate thatdosages may also be determined with guidance from Goodman & Gilman's ThePharmacological Basis of Therapeutics, Twelfth Edition (2011), AppendixII, pp. 1891-1991, and the Physicians' Desk Reference 70^(th) Edition,2016.

Pharmacogenomics

Pharmacogenomics is the methodology which associates genetic variabilitywith physiological and clinical responses to a drug. Pharmacogenetics isa subset of pharmacogenomics and is defined as “the study of variationsin DNA sequence as related to drug response” (ICH E15; see the WorldWide Webwww.fda.gov/downloads/RegulatoryInformation/Guidances/ucm129296.pdf).Pharmacogenetics often focuses on genetic polymorphisms in genes relatedto drug metabolism, drug mechanism of action, underlying disease type,and drug associated side effects. Pharmacogenetics is the cornerstone ofPersonalized Medicine which allows the development and the targeted useof drug therapies to obtain effective and safe treatment, as well as toadjust existing treatment regimens to further optimize the efficacy andsafety profile for the individual patient.

Pharmacogenetics has become a core component of many drug developmentprograms, being used to explain variability in drug response amongsubjects in clinical trials, to address unexpected emerging clinicalissues, such as adverse events, to determine eligibility for a clinicaltrial (pre-screening) to optimize trial yield, to develop drug companiondiagnostic tests to identify patients who are more likely or less likelyto benefit from treatment or who may be at risk of adverse events, toprovide information in drug labels to guide physician treatmentdecisions, to better understand the mechanism of action or metabolism ofnew and existing drugs, and to provide better understanding of diseasemechanisms as associated with treatment response.

Generally, pharmacogenetics analyses are often performed using thecandidate genes research technique, which is a hypothesis-drivenapproach, based on the detection of polymorphisms in candidate genespre-selected using knowledge of the disease, the drug's mode of action,toxicology, or metabolism of the drug.

Cardiovascular Disease Types and Causes

Cardiovascular disease, e.g., acute coronary events such as myocardialinfarction and stroke, is a class of disease that involves the heartand/or the blood vessels including the arteries and the veins. In theWestern world, cardiovascular disease, typically associated withunderlying atherosclerosis, is the leading cause of death(Martin-Ventura et al., 2009, Rev. Esp. Cardiol 62i6:677-688. citingMurray and Lopez, 1997, Lancet 349:1269-1276).

However, cardiovascular mortality in developed countries has decreasedsharply in recent decades (Tunstall-Pedoe, H., et al., Estimation ofcontribution of changes in coronary care to improving survival, eventrates, and coronary heart disease mortality across the WHO MONICAProject populations. Lancet, 2000. 355(9205): p. 688-700). This islikely due to the development and use of efficacious hypertension,thrombolytic, and lipid lowering therapies (Kuulasmaa, K., et al.,Estimation of contribution of changes in classic risk factors to trendsin coronary-event rates across the WHO MONICA Project). Nevertheless,cardiovascular diseases remain the major cause of death inindustrialized countries, at least in part due to the presence of highlyprevalent risk factors and insufficient treatment (Wong, M. D., et al.,Contribution of major diseases to disparities in mortality. N Engl JMed, 2002. 347(20): p. 1585-92). Even with appropriate therapy, not allpatients respond equally well to treatment. For example, despite theoverwhelming evidence that statins decrease risk for cardiovasculardisease, both in primary and secondary intervention settings, statintherapy clearly only achieves partial risk reduction. While a decreasein risk of 23 to 37% seen in the above trials is substantial andextremely important clinically, the majority of events still are notprevented by statin treatment. This is not surprising given thecomplexity of cardiovascular disease etiology, which is influenced bygenetics, family history, environment, and a variety of additional riskfactors including dyslipidemia, elevated cholesterol, age, gender,hypertension, diabetes, obesity, and smoking.

It is reasonable to assume that all of these multi-factorial risksmodify drug responses and determine the final benefit that eachindividual achieves from therapy. Furthermore, with the increasingincidence of Type 2 diabetes and obesity in Western countries (Flegal,K. M., et al., Prevalence and trends in obesity among US adults,1999-2000. Jama, 2002. 288(14): p. 1723-7, Boyle, J. P., et al.,Projection of diabetes burden through 2050: impact of changingdemography and disease prevalence in the U.S. Diabetes Care, 2001.24(11): p. 1936-40), which are two major risk factors for coronaryartery disease, and the emergence of greater cardiovascular risk factorsin the developing world (Yusuf, S., et al., Global burden ofcardiovascular diseases: Part II: variations in cardiovascular diseaseby specific ethnic groups and geographic regions and preventionstrategies. Circulation, 2001. 104(23): p. 2855-64, Yusuf, S., et alGlobal burden of cardiovascular diseases: part I: generalconsiderations, the epidemiologic transition, risk factors, and impactof urbanization. Circulation, 2001. 104(22): p. 2746-53), the need forever more effective treatment of cardiovascular disease is predicted tosteadily increase.

Atherosclerosis is a chronic disease process characterized by lipiddeposits and fibrosis of the intima, irregularly distributed in largeand medium sized arteries. The disease is progressive and most oftenbecomes clinically manifest in the middle-aged and elderly. When severe,the atherosclerotic plaque causes a reduction of the cross-sectionalarea of the arterial lumen, with and without thrombosis. Atheroscleroticplaques can occur in essentially any or all of the blood vessels of thebody, resulting in cardiovascular diseases involving the heart (e.g.,acute coronary syndrome, heart failure, and myocardial infarction), thebrain (e.g., stroke, transient ischemic attack, and brain infarction),the kidney (e.g., acute and chronic kidney disease, hypertension), andthe extremities (e.g., peripheral vascular disease, lower and/or upperextremity claudication, and lower and/or upper extremity ischemia).Resultant ischemic manifestations include: angina pectoris, rayocardialinfarction, stroke, intermittent claudication, gangrene of the lowerextremities, and renovascular hypertension.

Atherosclerosis may be considered as an aberrant form of wound-healingin arteries.

Atherosclerosis is considered by many to be an inflammatory disease. Inparticular, the lesions of atherosclerosis appear to represent a seriesof highly-specific cellular and molecular responses that can bedescribed as an inflammatory disease. See, e.g., Ross,“Atherosclerosis—An inflammatory disease” N Engl J Med (1999),340:115-126; the publications cited in Ross (1999); and subsequentpublications that cite Ross (1999); each of which is incorporated hereinin reference in its entirety.

A number of technologies have been developed to identify patients athigh risk for an adverse cardiac event. Coronary angiography has beenconsidered the “gold standard” but is invasive, costly, and subject tooperator-dependent variability (Sharma et al., 2010, Vase. Health RiskManag. 6:307-316). Other, less invasive options being explored includecoronary computed tomographic angiography (Sharma et al., supra; Cury etal., 2008. J. Nucl. Cardiol. 15 (4): 564-575). biomarkers (e.g.,Martin-Ventura et al., 2009, Rev. Esp. Cardiol 62(6):677-688), adenosinestress magnetic resonance (Ingkanisorn et al., 2006, J. Am. Coll.Cardiol. 47(7): 1427-1432). the use of clinical predictors (Tadros etal., 2003. South Med. J. 96(1 Γ):1113-1120; Schillinger et al., 2004,Wien Klin. Wochenschr. 116(3): 83-89), and indicators of plateletactivity (Marcucci et al., 2009, Circulation 119:237-242 (originallypublished online Dec. 31, 2008); Selvaraj et al., 2004, J. Throm.Thrombolysis 18(2): 109-115). Any of the above-mentioned technologiescan be combined with the present invention for diagnostic and treatmentpurposes of a subject with or suspected of having cardiovasculardisease.

Clinical Indicators

In the present invention, using the candidate genes research technique,a subject has his/her composite IL-1 genotype or IL-1 genotype patterndetermined (as disclosed herein). Additionally, s/he will have levels ofone or more clinical indicators measured. Non-limiting examples of theclinical indicators, include levels of Lp(a), OxPL, triglyceride-richlipoproteins, LDL-C, and CRP.

Based on the combination of which clinical indicators are elevated andthe subject's IL-1 genotype pattern a more aggressive and optimaltherapeutic intervention will be determined.

An individual may be administered a higher dose or a lower dose (e.g.,the dose of a single treatment and/or a daily dose comprising one ormore single treatments) of a particular drug depending on his/hercomposite IL-1 genotype or IL-1 genotype pattern; alternately, theindividual may be not given the particular drug depending on his/hercomposite IL-1 genotype or IL-1 genotype pattern and instead may beadministered another drug. For example, the other drug may operate by adifferent mode of action.

Alternately, the present invention may be used to optimize the size of aclinical trial.

For this, a study population is stratified by IL-1 pattern during orbefore randomization. This way, each group in a study will havesufficient numbers of members from each Pattern. This allows forsmaller-sized groups which can nonetheless be informative and providestatistical significance. Non-Caucasian ethnic/racial groups havedifferent frequencies for each pattern; thus, study populationscomprising Non-Caucasians may need to have their total population sizeadjusted accordingly.

Such stratification of clinical trial subjects may occur any timebefore, during, or after the clinical trial. In the latter case, forexample, if a clinical trial does not provide statistical significanceusing a general, non-stratified population, true statistical significantmay be later be discovered when the subject data is reconsidered andstratified by IL-1 pattern. That is, if the data of the clinical did notshow statistical evidence of a treatment response, the data could laterbe revaluated with consideration of IL-1 patterns. If so, it is possiblethat a previously “unsuccessful” clinical trial could be made“successful” when subjects are retroactively stratified by CIL-1pattern.

When subjects are stratified by IL-1 pattern, subjects of certainPatterns who will benefit from the treatment are identified and subjectsof other Patterns who will not benefit (or benefit less) from thetreatment are identified. Once the treatment is approved for clinicaluse, the stratified clinical trials will have revealed which patientpopulations (i.e., patients with a specific IL-1 pattern) should beprovided the treatment and which patients should not.

Difference Between the Present Invention and U.S. Pat. No. 6,210,877

U.S. Pat. No. 6,210,877, which is incorporated herein by reference inits entirety, relates to methods for diagnosing CVD using only complexIL-1 genotypes. On the other hand, the present invention relates todiagnosing and optimally treating a subject based upon a composite IL-1genotype or IL-1 genotype pattern and status of one or more clinicalindicators. More specifically the present application is based upon thatthere are certain activators that have a major causative effect onatherosclerotic cardiovascular disease by activating inflammatorycytokines, but the disease only reaches a level of clinical impact ifthe IL-1 genotypes amplify the inflammation to a magnitude that causesclinically significant damage. The disease therefore requires both anactivator, such as Lp(a), and the pro-inflammatory genotype. Given costand potential adverse events of drugs targeting the activators, the drugclinical value is conditional on the IL-1 genotype or a drug thatreduces the IL-1 amplification.

Ex Vivo Diagnostics

In aspects of the present invention, IL-1 levels can be measured ex vivoand in response to treatment with a therapeutic compound. For this,lymphocytes will be obtained from a subject. The lymphocytes will betreated with an IL-1 activator and then IL-1 levels (protein and/ormRNA) will be measured. If the lymphocytes produce increased IL-1 and toa critical level, then a diagnosis of the subject can be made and aprediction regarding an optimal treatment can be determined.

Isolated Nucleic Acid Molecules

As used herein, an “isolated nucleic acid molecule” generally is onethat contains one or more of the SNPs disclosed herein or one thathybridizes to such molecule such as a nucleic acid with a complementarysequence, and is separated from most other nucleic acids present in thenatural source of the nucleic acid molecule. As used herein, “anon-naturally occurring nucleic acid molecule” generally is one thatcontains one or more of the SNPs disclosed herein or one that hybridizesto such a molecule, such as a nucleic acid with a complementarysequence, but which does not correspond to a naturally occurringmolecule, e.g., it can be a molecule prepared by recombinant nucleicacid technology, chemical synthesis, or other synthetic means such aspolymerase chain reaction (PCR), and/or a nucleic acid which comprisesone or more synthetic components such as a non-natural nucleotide or anadded tag/motif.

The isolated nucleic acid may be obtained from any bodily fluid (such asblood, serum, plasma, urine, saliva, phlegm, gastric juices, semen,tears, sweat, etc.), skin, hair, cell (especially nucleated cells),biopsy, buccal swab, tissue, or tumor specimen. Alternately, theisolated nucleic acid may be amplified or synthesized from a nucleicacid obtained from any bodily fluid, skin, hair, cell, biopsy, buccalswab, tissue, or tumor specimen.

Generally, an isolated SNP-containing nucleic acid molecule includes oneor more of SNPs and/or one or more SNPs in linkage disequilibrium withone or more SNPs. The isolated SNP-containing nucleic acid molecule mayinclude flanking nucleotide sequences on either side of the SNPposition. A flanking sequence can include nucleotide residues that arenaturally associated with the SNP site and/or heterologous nucleotidesequences. Preferably, the flanking sequence is up to about 10,000,1,000, 500, 300, 100, 60, 50, 30, 25, 20, 15, 10, 8, or 4 nucleotides(or any other length in-between) on either side of a SNP position, or aslong as the full-length gene, entire protein-coding sequence (or anyportion thereof such as an exon), entire enhancer/promoter region orportion thereof, or entire intron or portion thereof.

An isolated SNP-containing nucleic acid molecule can include, forexample, a full-length gene or transcript, such as a gene isolated fromgenomic DNA (e.g., by cloning or PCR amplification), a cDNA molecule, oran mRNA transcript molecule.

An isolated nucleic acid molecule of the disclosed subject matterfurther encompasses a SNP-containing polynucleotide that is the productof any one of a variety of nucleic acid amplification methods, which areused to increase the copy numbers of a polynucleotide of interest in anucleic acid sample. Such amplification methods are well known in theart, and they include but are not limited to, polymerase chain reaction(PCR) (U.S. Pat. Nos. 4,683,195 and 4,683,202; PCR Technology:Principles and Applications for DNA Amplification, ed. H. A. Erlich,Freeman Press, NY, N.Y. (1992)), ligase chain reaction (LCR) (Wu andWallace, Genomics 4:560 (1989); Landegren et al., Science 241:1077(1988)), strand displacement amplification (SDA) (U.S. Pat. Nos.5,270,184 and 5,422,252), transcription-mediated amplification (TMA)(U.S. Pat. No. 5,399,491), linked linear amplification (LLA) (U.S. Pat.No. 6,027,923) and the like, and isothermal amplification methods suchas nucleic acid sequence based amplification (NASBA) and self-sustainedsequence replication (Guatelli et al., Proc Natl Acad Sci USA 87:1874(1990)). Based on such methodologies, a person skilled in the art canreadily design primers in any suitable regions 5′ and 3′ to a SNPdisclosed herein. Such primers may be used to amplify DNA of any lengthso long that it contains the SNP of interest in its sequence.

The isolated nucleic acid molecules that include, consist of, or consistessentially of one or more polynucleotide sequences that contain one ormore SNPs disclosed herein, complements thereof, SNPs in linkagedisequilibrium with the SNPs disclosed herein, and/or SNP-containingfragments thereof. Non-limiting examples of SNPs in linkagedisequilibrium with the SNPs disclosed herein include those listed inthe Table below.

Linkage SNP Common SNP Rsquared rs16944 B(−511) rs1143627 0.965rs13013349 0.964 rs1143623 0.827 rs1143623 B(−1464) rs12621220 0.963rs1143627 0.864 rs13008855 0.857 rs16944 0.827 rs12053091 0.824 rs484306B(−3737) None rs17561 A(+4845) rs3783557 0.961 rs11898680 0.821 A(−889)rs1800587 rs1143634 B(+3954) rs3917373 0.881

Isolated nucleic acid molecules can be in the form of RNA, such as mRNA,or in the form DNA, including cDNA and genomic DNA, which may beobtained, for example, by molecular cloning or produced by chemicalsynthetic techniques or by a combination thereof. Sambrook and Russell,Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, N.Y.(2000). Furthermore, isolated nucleic acid molecules, particularly SNPdetection reagents such as probes and primers, can also be partially orcompletely in the form of one or more types of nucleic acid analogs,such as peptide nucleic acid (PNA). U.S. Pat. Nos. 5,539,082; 5,527,675;5,623,049; and 5,714,331. The nucleic acid, especially DNA, can bedouble-stranded or single-stranded. Single-stranded nucleic acid can bethe coding strand (sense strand) or the complementary non-coding strand(anti-sense strand). DNA, RNA, or PNA segments can be assembled, forexample, from fragments of the human genome (in the case of DNA or RNA)or single nucleotides, short oligonucleotide linkers, or from a seriesof oligonucleotides, to provide a synthetic nucleic acid molecule.Nucleic acid molecules can be readily synthesized using the sequencesprovided herein as a reference; oligonucleotide and PNA oligomersynthesis techniques are well known in the art. See, e.g., Corey,“Peptide nucleic acids: expanding the scope of nucleic acidrecognition,” Trends Biotechnol 15 (6):224-9 (June 1997), and Hyrup etal., “Peptide nucleic acids (PNA): synthesis, properties and potentialapplications,” Bioorg Med Chem 4 (1):5-23 (January 1996). Furthermore,large-scale automated oligonucleotide/PNA synthesis (including synthesison an array or bead surface or other solid support) can readily beaccomplished using commercially available nucleic acid synthesizers,such as the Applied Biosystems (Foster City, Calif.) 3900High-Throughput DNA Synthesizer or Expedite 8909 Nucleic Acid SynthesisSystem and the sequence information provided herein.

The isolated SNP-containing nucleic acid molecule may comprise modified,synthetic, or non-naturally occurring nucleotides or structural elementsor other alternative/modified nucleic acid chemistries known in the art.Such nucleic acid analogs are useful, for example, as detection reagents(e.g., primers/probes) for detecting the SNPs identified herein.Furthermore, kits/systems (such as beads, arrays, etc.) that includethese analogs are also encompassed herein.

The practice of the present methods will employ, unless otherwiseindicated, conventional techniques of cell biology, cell culture,molecular biology, transgenic biology, microbiology, recombinant DNA,and immunology, which are within the skill of the art. Such techniquesare explained fully in the literature. See, for example, MolecularCloning: A Laboratory Manual, Cold Spring Harbor Laboratory (2001); DNACloning, Volumes I and II (P. N. Glover ed., 1985); OligonucleotideSynthesis (M. J. Gait ed., 1984); Mullis et al. U.S. Pat. No. 4,683,195;Nucleic Acid Hybridization (B. D. Hames & S. J. Higgins eds. 1984);Transcription And Translation (B. Q. Hames & S. J. Higgins eds. 1984);Culture Of Animal Cells (R. I. Freshney, Alan R. Liss, Inc., 1987);Immobilized Cells And Enzymes (IRL Press, 1986); B. Perbal, A PracticalGuide To Molecular Cloning (1984); the treatise, Methods In Enzymology(Academic Press, Inc., N.Y.); Gene Transfer Vectors For Mammalian Cells(J. H. Miller and M. P. Calos eds., 1987, Cold Spring HarborLaboratory); Methods In Enzymology, Vols. 154 and 155 (Wu at al. eds.),Immunochemical Methods In Cell And Molecular Biology (Mayer and Walker,eds., Academic Press, London, 1987); Handbook Of ExperimentalImmunology, Volumes I-IV (D. M. Weir and C. C. Blackwell, eds., 1986);Manipulating the Mouse Embryo, (Cold Spring Harbor Laboratory Press,Cold Spring Harbor, N.Y., 1986).

SNP Detection Reagents

In aspects of the present invention, each of the one or more of the SNPsdisclosed herein can be used for the design of SNP detection reagents.As used herein, a “SNP detection reagent” is a reagent that specificallydetects a specific target SNP position disclosed herein, and that ispreferably specific for a particular nucleotide (allele) of the targetSNP position (i.e., the detection reagent preferably can differentiatebetween different alternative nucleotides at a target SNP position,thereby allowing the identity of the nucleotide present at the targetSNP position to be determined). Typically, such detection reagenthybridizes to a target SNP-containing nucleic acid molecule bycomplementary base-pairing in a sequence specific manner, anddiscriminates the target variant sequence from other nucleic acidsequences such as an art-known form in a test sample. An example of adetection reagent is a non-naturally occurring nucleic acid probe thathybridizes to a target nucleic acid containing one of the SNPs disclosedherein. In a preferred embodiment, such a probe can differentiatebetween nucleic acids having a particular nucleotide (allele) at thetarget SNP position from other nucleic acids that have a differentnucleotide at the same target SNP position. In addition, a detectionreagent may hybridize to a specific region 5′ and/or 3′ to the SNPposition.

Another example of a detection reagent is a non-naturally occurringnucleic acid primer that acts as an initiation point of nucleotideextension along a complementary strand of a target polynucleotide. TheSNP sequence information provided herein is also useful for designingprimers, e.g., allele-specific primers, to amplify (e.g., using PCR) theSNP of the disclosed subject matter.

A SNP detection reagent may be an isolated or synthetic DNA or RNApolynucleotide probe or primer or PNA oligomer, or a combination of DNA,RNA and/or PNA that hybridizes to a segment of a target nucleic acidmolecule containing one of the SNPs disclosed herein. A detectionreagent in the form of a non-naturally occurring polynucleotide mayoptionally contain modified base analogs, intercalators, or minor groovebinders. Multiple detection reagents such as probes may be, for example,affixed to a solid support (e.g., an array and bead) or supplied insolution (e.g., probe/primer sets for enzymatic reactions such as PCR,RT-PCR, TaqMan® assays, and primer-extension reactions) to form a SNPdetection kit.

For analyzing SNPs, it can be appropriate to use oligonucleotidesspecific for alternative SNP alleles. Such oligonucleotides that detectsingle nucleotide variations in target sequences may be referred to bysuch terms as “allele-specific oligonucleotides,” “allele-specificprobes,” or “allele-specific primers.” The design and use ofallele-specific probes for analyzing polymorphisms is described in,e.g., Mutation Detection: A Practical Approach, Cotton et al., eds.,Oxford University Press (1998); Saiki et al., Nature 324:163-166 (1986);Dattagupta, EP235,726; and Saiki, WO 89/11548.

In another embodiment, a probe or primer may be designed to hybridize toa segment of target DNA such that the SNP aligns with either the 5′-mostend or the 3′-most end of the probe or primer. When using anoligonucleotide ligation assay (U.S. Pat. No. 4,988,617), the 3′ mostnucleotide of the probe aligns with the SNP position in the targetsequence.

Allele-specific probes are often used in pairs (or, less commonly, insets of 3 or 4), and such pairs may be identical except for a onenucleotide mismatch that represents the allelic variants at the SNPposition. Typically, one member of a probe pair perfectly matches areference form of a target sequence that has a more common SNP allele(i.e., the allele that is more frequent in the target population) andthe other member of the pair perfectly matches a form of the targetsequence that has a less common SNP allele (i.e., the allele that israrer in the target population). In the case of an array, multiple pairsof probes can be immobilized on the same support for simultaneousanalysis of multiple different polymorphisms.

In one type of PCR-based assay, an allele-specific primer hybridizes toa region on a target nucleic acid molecule that overlaps a SNP positionand only primes amplification of an allelic form to which the primerexhibits perfect complementarity. Gibbs, Nucleic Acid Res 17:2427-2448(1989). Typically, the primer's 3′-most nucleotide is aligned with andcomplementary to the SNP position of the target nucleic acid molecule.This primer is used in conjunction with a second primer that hybridizesat a distal site. Amplification proceeds from the two primers, producinga detectable product that indicates which allelic form is present in thetest sample. A control is usually performed with a second pair ofprimers, one of which shows a single base mismatch at the polymorphicsite and the other of which exhibits perfect complementarity to a distalsite. The single-base mismatch prevents amplification or substantiallyreduces amplification efficiency, so that either no detectable productis formed or it is formed in lower amounts or at a slower pace. Themethod generally works most effectively when the mismatch is at the3′-most position of the oligonucleotide (i.e., the 3′-most position ofthe oligonucleotide aligns with the target SNP position) because thisposition is most destabilizing to elongation from the primer (see, e.g.,WO 93/22456). This PCR-based assay can be utilized as part of theTaqMan® assay, described below.

A primer may contain a sequence substantially complementary to a segmentof a target SNP-containing nucleic acid molecule except that the primerhas a mismatched nucleotide in one of the three nucleotide positions atthe 3′-most end of the primer, such that the mismatched nucleotide doesnot base pair with a particular allele at the SNP site. In a preferredembodiment, the mismatched nucleotide in the primer is the second fromthe last nucleotide at the 3′-most position of the primer. In a morepreferred embodiment, the mismatched nucleotide in the primer is thelast nucleotide at the 3′-most position of the primer.

A SNP detection reagent may be labeled with a fluorogenic reporter dyethat emits a detectable signal. While the preferred reporter dye is afluorescent dye, any reporter dye that can be attached to a detectionreagent such as an oligonucleotide probe or primer is suitable for usein the disclosed subject matter. Such dyes include, but are not limitedto, Acridine, AMCA, BODIPY, Cascade Blue, Cy2, Cy3, Cy5, Cy7, Dabcyl,Edans, Eosin, Erythrosin, Fluorescein, 6-Fam, Tet, Joe, Hex, OregonGreen, Rhodamine, Rhodol Green, Tamra, Rox, and Texas Red.

In yet another embodiment, the detection reagent may be further labeledwith a quencher dye such as TAMRA, especially when the reagent is usedas a self-quenching probe such as a TaqMan® (U.S. Pat. Nos. 5,210,015and 5,538,848) or Molecular Beacon probe (U.S. Pat. Nos. 5,118,801 and5,312,728), or other stemless or linear beacon probe (Livak et al., PCRMethod Appl 4:357-362 (1995); Tyagi et al., Nature Biotechnology14:303-308 (1996); Nazarenko et al., Nuc' Acids Res 25:2516-2521 (1997);U.S. Pat. Nos. 5,866,336 and 6,117,635.

Detection reagents may also contain other labels, including but notlimited to, biotin for streptavidin binding, hapten for antibodybinding, and an oligonucleotide for binding to another complementaryoligonucleotide.

Reagents may not contain (or be complementary to) a SNP nucleotide asdescribe herein but that are used to assay one or more SNPs disclosedherein. For example, primers that flank, but do not hybridize directlyto a target SNP position provided herein are useful in primer extensionreactions in which the primers hybridize to a region adjacent to thetarget SNP position (i.e., within one or more nucleotides from thetarget SNP site). During the primer extension reaction, a primer istypically not able to extend past a target SNP site if a particularnucleotide (allele) is present at that target SNP site, and the primerextension product can be detected in order to determine which SNP alleleis present at the target SNP site. For example, particular ddNTPs aretypically used in the primer extension reaction to terminate primerextension once a ddNTP is incorporated into the extension product (aprimer extension product which includes a ddNTP at the Y-most end of theprimer extension product, and in which the ddNTP is a nucleotide of aSNP disclosed herein, is a composition that is specifically herein).Thus, reagents that bind to a nucleic acid molecule in a region adjacentto a SNP site and that are used for assaying the SNP site, even thoughthe bound sequences do not necessarily include the SNP site itself, arealso contemplated by the disclosed subject matter.

For example, the SNP may be identified using single-base extension(SBE). SBE determines the identity of a nucleotide base at a specificposition along a nucleic acid. In the method, an oligonucleotide primerhybridizes to a complementary region along the nucleic acid, to form aduplex, with the primer's terminal 3′ end directly adjacent to thenucleotide base to be identified. The oligonucleotide primer isenzymatically extended by a single base in the presence of all fournucleotide terminators; the nucleotide terminator complementary to thebase in the template being interrogated is incorporated and identified.The presence of all four terminators ensures that no further extensionoccurs beyond the single incorporated base. Many approaches can be takenfor determining the identity of a terminator, including fluorescencelabeling, mass labeling for mass spectrometry, measuring enzyme activityusing a protein moiety, and isotope labeling.

Reagents and techniques described herein may be directed to performanceof “Next Generation Sequencing.” (See, e.g., Srivatsan et al., PLoSGenet 4: e100139 (2008); Rasmussen et al., Nature 463:757-762 (2010); Liet al., Nature 463: 311-317 (2010); Pelak et al., PLoS Genet 6: e1001111(2010); Ram et al., Syst Biol Reprod Med (57(3):117-118 (2011);McEllistrem, Future Microbiol 4: 857-865 (2009); Lo et al., Clin Chem55: 607-608 (2009); Robinson, Genome Biol 11:144 (2010); and Araya etal., Trends Biotechnology doi10. 1016.j.tibtech.2011.04.003 (2011)). Forexample, such techniques may involve the fragmentation of a genomicnucleic acid sample followed by parallel sequencing of those fragmentsand the alignment of the sequenced fragments to reconstruct the originalsequence. Here, the genomic nucleic acid of interest is sheared intofragments and “adapters” (short nucleic acids of known sequence) areligated to the fragments. Adaptor-modified fragments can be enriched viaPCR. An adaptor-modified fragment (and amplified copies thereof, ifpresent) may be flowed across a flow cell where the fragments areallowed to hybridize to primers immobilized on the surface of the cell.The fragments are then amplified by isothermal bridge amplification intoa cluster consisting of thousands of molecules identical to theoriginal. Sequencing primers can then be hybridized to the ends of onestrand of the clusters, reversibly blocked, and labeled nucleotidesadded. The addition of each particular nucleotide can be identified bythe label, then the label can be removed and the nucleotide un-blockedso that another blocked and labeled nucleotide can be added to identifythe next position in the nucleic acid sequence. Once the desired numberof rounds of addition, detection, and unblocking occur, the resultingsequences can be aligned.

It will be apparent to one of skill in the art that such primers andprobes are directly useful as reagents for detecting the SNPs of thedisclosed subject matter, and can be incorporated into any kit/systemformat.

SNP Genotyping Methods

SNP genotyping includes, for example, collecting a biological samplefrom a human subject (e.g., sample of tissues, cells, fluids,secretions, etc.), isolating nucleic acids (e.g., genomic DNA, mRNA orboth) from the cells of the sample, contacting the nucleic acids withone or more primers which specifically hybridize to a region of theisolated nucleic acid containing a target SNP under conditions such thathybridization and amplification of the target nucleic acid regionoccurs, and determining the nucleotide present at the SNP position ofinterest, or, in some assays, detecting the presence or absence of anamplification product (assays can be designed so that hybridizationand/or amplification will only occur if a particular SNP allele ispresent or absent). In some assays, the size of the amplificationproduct is detected and compared to the length of a control sample; forexample, deletions and insertions can be detected by a change in size ofthe amplified product compared to a normal genotype.

SNP genotyping is useful for numerous practical applications, asdescribed herein. Examples of such applications include, but are notlimited to, SNP-disease association analysis, disease predispositionscreening, disease diagnosis, disease prognosis, disease progressionmonitoring, determining therapeutic strategies based on an individual'sgenotype (“pharmacogenomics”), developing therapeutic agents based onSNP genotypes associated with a disease or likelihood of responding to adrug, stratifying patient populations for clinical trials of atherapeutic, preventive, or diagnostic agent, and human identificationapplications such as forensics.

Nucleic acid samples can be genotyped to determine which allele ispresent at any given SNP position of interest by methods well known inthe art. The neighboring sequence can be used to design SNP detectionreagents such as oligonucleotide probes, which may optionally beimplemented in a kit format. Exemplary SNP genotyping methods aredescribed in Chen et al., “Single nucleotide polymorphism genotyping:biochemistry, protocol, cost and throughput,” Pharmacogenomics J 3(2):77-96 (2003); Kwok et al., “Detection of single nucleotidepolymorphisms,” Curr Issues Mol Biol 5 (2):43-60 (April 2003); Shi,“Technologies for individual genotyping: detection of geneticpolymorphisms in drug targets and disease genes,” Am J Pharmacogenomics2 (3):197-205 (2002); and Kwok, “Methods for genotyping singlenucleotide polymorphisms,” Annu Rev Genom Hum Genet 2:235-58 (2001).Techniques for high-throughput SNP genotyping are described in Mamellos,“High-throughput SNP analysis for genetic association studies,” CurrOpin Drug Disc Devel 6 (3):317-21 (May 2003).

SNP genotyping methods include, but are not limited to, TaqMan® assays,molecular beacon assays, nucleic acid arrays, allele-specific primerextension, allele-specific PCR, arrayed primer extension, homogeneousprimer extension assays, primer extension with detection by massspectrometry, pyrosequencing, multiplex primer extension sorted ongenetic arrays, ligation with rolling circle amplification, homogeneousligation, Oligonucleotide Ligation Assay (OLA: U.S. Pat. No. 4,988,167),multiplex ligation reaction sorted on genetic arrays,restriction-fragment length polymorphism, single base extension-tagassays, denaturing gradient gel electrophoresis, and the Invader assay.Such methods may be used in combination with detection mechanisms suchas, for example, luminescence or chemiluminescence detection,fluorescence detection, time-resolved fluorescence detection,fluorescence resonance energy transfer, fluorescence polarization, massspectrometry, and electrical detection.

In one embodiment, SNP genotyping is performed using the TaqMan® assay,which is also known as the 5′ nuclease assay (U.S. Pat. Nos. 5,210,015and 5,538,848). The TaqMan® assay detects the accumulation of a specificamplified product during PCR. The TaqMan® assay utilizes anoligonucleotide probe labeled with a fluorescent reporter dye and aquencher dye. The reporter dye is excited by irradiation at anappropriate wavelength, it transfers energy to the quencher dye in thesame probe via a process called fluorescence resonance energy transfer(FRET). When attached to the probe, the excited reporter dye does notemit a signal. The proximity of the quencher dye to the reporter dye inthe intact probe maintains a reduced fluorescence for the reporter. Thereporter dye and quencher dye may be at the 5′ most and the 3′ mostends, respectively, or vice versa. Alternatively, the reporter dye maybe at the 5′ or 3′ most end while the quencher dye is attached to aninternal nucleotide, or vice versa. In yet another embodiment, both thereporter and the quencher may be attached to internal nucleotides at adistance from each other such that fluorescence of the reporter isreduced.

During PCR, the 5′ nuclease activity of DNA polymerase cleaves theprobe, thereby separating the reporter dye and the quencher dye andresulting in increased fluorescence of the reporter. Accumulation of PCRproduct is detected directly by monitoring the increase in fluorescenceof the reporter dye. The DNA polymerase cleaves the probe between thereporter dye and the quencher dye only if the probe hybridizes to thetarget SNP-containing template which is amplified during PCR, and theprobe is designed to hybridize to the target SNP site only if aparticular SNP allele is present.

Preferred TaqMan® primer and probe sequences can readily be determinedusing the SNP and associated nucleic acid sequence information providedherein. A number of computer programs, such as Primer Express (AppliedBiosystems, Foster City, Calif.), can be used to rapidly obtain optimalprimer/probe sets. These probes and primers can be readily incorporatedinto a kit format. The disclosed subject matter also includesmodifications of the TaqMan® assay well known in the art such as the useof Molecular Beacon probes (U.S. Pat. Nos. 5,118,801 and 5,312,728) andother variant formats (U.S. Pat. Nos. 5,866,336 and 6,117,635).

Another method for genotyping the SNPs can be the use of twooligonucleotide probes in an OLA (see, e.g., U.S. Pat. No. 4,988,617).In this method, one probe hybridizes to a segment of a target nucleicacid with its 3′ most end aligned with the SNP site. A second probehybridizes to an adjacent segment of the target nucleic acid moleculedirectly 3′ to the first probe. The two juxtaposed probes hybridize tothe target nucleic acid molecule, and are ligated in the presence of alinking agent such as a ligase if there is perfect complementaritybetween the 3′ most nucleotide of the first probe with the SNP site. Ifthere is a mismatch, ligation would not occur. After the reaction, theligated probes are separated from the target nucleic acid molecule, anddetected as indicators of the presence of a SNP.

The following patents, patent applications, and published internationalpatent applications, which are all hereby incorporated by reference,provide additional information pertaining to techniques for carrying outvarious types of Oligonucleotide Ligation Assay (OLA). The followingU.S. patents describe OLA strategies for performing SNP detection: U.S.Pat. Nos. 6,027,889; 6,268,148; 5,494,810; 5,830,711 and 6,054,564. WO97/31256 and WO 00/56927 describe OLA strategies for performing SNPdetection using universal arrays, where a zipcode sequence can beintroduced into one of the hybridization probes, and the resultingproduct, or amplified product, hybridized to a universal zip code array.U.S. application Ser. No. 01/17,329 (and Ser. No. 09/584,905) describesOLA (or LDR) followed by PCR, where zipcodes are incorporated into OLAprobes, and amplified PCR products are determined by electrophoretic oruniversal zipcode array readout. U.S. applications 60/427,818,60/445,636, and 60/445,494 describe SNPIex methods and software formultiplexed SNP detection using OLA followed by PCR, where zipcodes areincorporated into OLA probes, and amplified PCR products are hybridizedwith a zipchute reagent, and the identity of the SNP determined fromelectrophoretic readout of the zipchute. In some embodiments, OLA iscarried out prior to PCR (or another method of nucleic acidamplification). In other embodiments, PCR (or another method of nucleicacid amplification) is carried out prior to OLA.

Another method for SNP genotyping is based on mass spectrometry. Massspectrometry takes advantage of the unique mass of each of the fournucleotides of DNA. SNPs can be unambiguously genotyped by massspectrometry by measuring the differences in the mass of nucleic acidshaving alternative SNP alleles. MALDI-TOF (Matrix Assisted LaserDesorption Ionization-Time of Flight) mass spectrometry technology ispreferred for extremely precise determinations of molecular mass, suchas SNPs. Numerous approaches to SNP analysis have been developed basedon mass spectrometry. Preferred mass spectrometry-based methods of SNPgenotyping include primer extension assays, which can also be utilizedin combination with other approaches, such as traditional gel-basedformats and microarrays.

Typically, a mass spectrometry with primer extension assay involvesdesigning and annealing a primer to a template PCR amplicon upstream(5′) from a target SNP position. A mix of dideoxynucleotidetriphosphates (ddNTPs) and/or deoxynucleotide triphosphates (dNTPs) areadded to a reaction mixture containing template (e.g., a SNP-containingnucleic acid molecule which has typically been amplified, such as byPCR), primer, and DNA polymerase. Extension of the primer terminates atthe first position in the template where a nucleotide complementary toone of the ddNTPs in the mix occurs. The primer can be eitherimmediately adjacent (i.e., the nucleotide at the 3′ end of the primerhybridizes to the nucleotide next to the target SNP site) or two or morenucleotides removed from the SNP position. If the primer is severalnucleotides removed from the target SNP position, the only limitation isthat the template sequence between the 3′ end of the primer and the SNPposition cannot contain a nucleotide of the same type as the one to bedetected, or this will cause premature termination of the extensionprimer. Alternatively, if all four ddNTPs alone, with no dNTPs, areadded to the reaction mixture, the primer will always be extended byonly one nucleotide, corresponding to the target SNP position. In thisinstance, primers are designed to bind one nucleotide upstream from theSNP position (i.e., the nucleotide at the 3′ end of the primerhybridizes to the nucleotide that is immediately adjacent to the targetSNP site on the 5′ side of the target SNP site). Extension by only onenucleotide is preferable, as it minimizes the overall mass of theextended primer, thereby increasing the resolution of mass differencesbetween alternative SNP nucleotides. Furthermore, mass-tagged ddNTPs canbe employed in the primer extension reactions in place of unmodifiedddNTPs. This increases the mass difference between primers extended withthese ddNTPs, thereby providing increased sensitivity and accuracy, andis particularly useful for typing heterozygous base positions.

Primer extension assays may be used in conjunction with MALDI-TOF massspectrometry for SNP genotyping, see, e.g., Wise et al., “A standardprotocol for single nucleotide primer extension in the human genomeusing matrix-assisted laser desorption/ionization time-of-flight massspectrometry,” Rapid Comm. Mass Spect. 17 (11):1195-202 (2003).

SNPs can also be scored by direct DNA sequencing. A variety of automatedsequencing procedures can be utilized (e.g., Biotechniques 19:448(1995)), including sequencing by mass spectrometry. See, e.g., PCTInternational Publication No. WO 94/16101; Cohen et al., Adv Chromatogr36:127-162 (1996); and Griffin et al, Appl Biochem Biotechnol 38:147-159(1993). The nucleic acid sequences of the disclosed subject matterenable one of ordinary skill in the art to readily design sequencingprimers for such automated sequencing procedures. Commercialinstrumentation, such as the Applied Biosystems 377, 3100, 3700, 3730,and 3730×1 DNA Analyzers (Foster City, Calif.), is commonly used in theart for automated sequencing.

Other methods that can be used to genotype the SNPs of the disclosedsubject matter include single-strand conformational polymorphism (SSCP),and denaturing gradient gel electrophoresis (DGGE). Myers et al., Nature313:495 (1985). SSCP identifies base differences by alteration inelectrophoretic migration of single stranded PCR products, as describedin Orita et al., Proc. Nat. Acad. Single-stranded PCR products can begenerated by heating or otherwise denaturing double stranded PCRproducts. Single-stranded nucleic acids may refold or form secondarystructures that are partially dependent on the base sequence. Thedifferent electrophoretic mobilities of single-stranded amplificationproducts are related to base-sequence differences at SNP positions. DGGEdifferentiates SNP alleles based on the different sequence-dependentstabilities and melting properties inherent in polymorphic DNA and thecorresponding differences in electrophoretic migration patterns in adenaturing gradient gel. PCR Technology: Principles and Applications forDNA Amplification Chapter 7, Erlich, ed., W.H. Freeman and Co, N.Y.(1992).

Sequence-specific ribozymes (U.S. Pat. No. 5,498,531) can also be usedto score SNPs based on the development or loss of a ribozyme cleavagesite. Perfectly matched sequences can be distinguished from mismatchedsequences by nuclease cleavage digestion assays or by differences inmelting temperature. If the SNP affects a restriction enzyme cleavagesite, the SNP can be identified by alterations in restriction enzymedigestion patterns, and the corresponding changes in nucleic acidfragment lengths determined by gel electrophoresis.

SNP Detection Kits and Systems

A person skilled in the art will recognize that, based on the SNP andassociated sequence information disclosed herein, detection reagents canbe developed and used to assay the SNP of the disclosed subject matterindividually or in combination with other SNPs, and such detectionreagents can be readily incorporated into one of the established kit orsystem formats which are well known in the art.

The terms “kits” and “systems,” as used herein in the context of SNPdetection reagents, are intended to refer to such things as combinationsof multiple SNP detection reagents, or one or more SNP detectionreagents in combination with one or more other types of elements orcomponents (e.g., other types of biochemical reagents, containers,packages such as packaging intended for commercial sale, substrates towhich SNP detection reagents are attached, electronic hardwarecomponents, and software recorded on a non-transitory processor-readablemedium). Accordingly, the disclosed subject matter further provides SNPdetection kits and systems, including but not limited to, packaged probeand primer sets (e.g., TaqMan® probe/primer sets), arrays/microarrays ofnucleic acid molecules, and beads that contain one or more probes,primers, or other detection reagents for detecting one or more SNPs ofthe disclosed subject matter.

The kits/systems can optionally include various electronic hardwarecomponents; for example, arrays (“DNA chips”) and microfluidic systems(“lab-on-a-chip” systems) provided by various manufacturers typicallyinclude hardware components. Other kits/systems (e.g., probe/primersets) may not include electronic hardware components, but may include,for example, one or more SNP detection reagents (along with, optionally,other biochemical reagents) packaged in one or more containers.

In some embodiments, a SNP detection kit typically contains one or moredetection reagents and other components (e.g., a buffer, enzymes such asDNA polymerases or ligases, chain extension nucleotides such asdeoxynucleotide triphosphates, and in the case of Sanger-type DNAsequencing reactions, chain terminating nucleotides, positive controlsequences, negative control sequences, and the like) necessary to carryout an assay or reaction, such as amplification and/or detection of aSNP-containing nucleic acid molecule.

A kit may further contain instructions for using the kit to detect theSNP-containing nucleic acid molecule of interest.

The instructions may include information which allows a user to identifywhether an individual having or suspected of having aninflammation-related cardiovascular disorder/disease hasgenotype-specific differential expression of IL-1, i.e., is a “high” or“low” producer of IL-1, based upon the composite IL-1 genotype or IL-1genotype patterns disclosed in Table 1 and Table 2 and has a relevantstatus of one or more clinical indicators, as disclosed herein. Theinstructions may include information which allows a user to decide on anappropriate drug or drugs (e.g., as disclosed in Table 3 to Table 7and/or an alternate drug having a similar or identical mode of action asa drug disclosed in Table 3 to Table 7) and at an appropriate dose.

In one embodiment, kits are provided which contain the necessaryreagents to carry out one or more assays to detect one or more SNPsdisclosed herein. In another embodiment, SNP detection kits/systems arein the form of nucleic acid arrays, or compartmentalized kits, includingmicrofluidic/lab-on-a-chip systems.

SNP detection kits/systems may contain, for example, one or more probes,or pairs of probes, that hybridize to a nucleic acid molecule at or neareach target SNP position. Multiple pairs of allele-specific probes maybe included in the kit/system to simultaneously assay large numbers ofSNPs, at least one of which is the SNP of the disclosed subject matter.In some kits/systems, the allele-specific probes are immobilized to asubstrate such as an array or bead.

The terms “arrays,” “microarrays,” and “DNA chips” are used hereininterchangeably to refer to an array of distinct polynucleotides affixedto a substrate, such as glass, plastic, paper, nylon or other type ofmembrane, filter, chip, or any other suitable solid support. Thepolynucleotides can be synthesized directly on the substrate, orsynthesized separate from the substrate and then affixed to thesubstrate.

Any number of probes, such as allele-specific probes, may be implementedin an array, and each probe or pair of probes can hybridize to adifferent SNP position. In the case of polynucleotide probes, they canbe synthesized at designated areas (or synthesized separately and thenaffixed to designated areas) on a substrate using a light-directedchemical process. Each DNA chip can contain, for example, thousands tomillions of individual synthetic polynucleotide probes arranged in agrid-like pattern and miniaturized (e.g., to the size of a dime).Preferably, probes are attached to a solid support in an ordered,addressable array.

A SNP detection kit/system can include components that are used toprepare nucleic acids from a test sample for the subsequentamplification and/or detection of a SNP-containing nucleic acidmolecule. Such sample preparation components can be used to producenucleic acid extracts (including DNA and/or RNA), proteins or membraneextracts from any bodily fluids (such as blood, serum, plasma, urine,saliva, phlegm, gastric juices, semen, tears, sweat, etc.), skin, hair,cells (especially nucleated cells), biopsies, buccal swabs or tissue ortumor specimens. Methods of preparing nucleic acids, proteins, and cellextracts are well known in the art and can be readily adapted to obtaina sample that is compatible with the system utilized. Automated samplepreparation systems for extracting nucleic acids from a test sample arecommercially available, and examples are Qiagen's BioRobot 9600, AppliedBiosystems' PRISM 6700 sample preparation system, and Roche MolecularSystems' COBAS AmpliPrep System.

For genotyping SNPs, an exemplary microfluidic system may integrate, forexample, nucleic acid amplification, primer extension, capillaryelectrophoresis, and a detection method such as laser inducedfluorescence detection. In an exemplary process for using such anexemplary system, nucleic acid samples are amplified, preferably by PCR.Then, the amplification products are subjected to automated primerextension reactions using ddNTPs (specific fluorescence for each ddNTP)and the appropriate oligonucleotide primers to carry out primerextension reactions which hybridize just upstream of the targeted SNP.Once the extension at the 3′ end is completed, the primers are separatedfrom the unincorporated fluorescent ddNTPs by capillary electrophoresis.The separation medium used in capillary electrophoresis can be, forexample, polyacrylamide, polyethyleneglycol or dextran. The incorporatedddNTPs in the single nucleotide primer extension products are identifiedby laser-induced fluorescence detection. Such an exemplary microchip canbe used to process, for example, at least 96 to 384 samples, or more, inparallel.

An exemplary kit allows a user to determine whether a subject hasgenotype-specific differential expression of IL-1, i.e., is a “high” or“low” producer of IL-1, based upon the composite IL-1 genotype or IL-1genotype patterns disclosed in Table 1 and Table 2 and has a relevantstatus of one or more clinical indicators, as disclosed herein. Theexemplary kit may include instructions having information which allows auser to decide on an appropriate drug or drugs (e.g., as disclosed inTable 3 to Table 7 and/or an alternate drug(s) having a similar oridentical mode of action as a drug disclosed in Table 3 to Table 7) andat an appropriate dose.

Reports, Programmed Computers, and Systems

The results of a test provide an identification of a composite IL-1genotype or IL-1 genotype pattern, as disclosed in Table 1 and Table 2and identification of the status for one or more clinical indicators, asdisclosed herein, which together determine an individual's predicteddrug responsiveness (e.g., response of a drug or drugs disclosed inTable 3 to Table 7 and/or an alternate drug having a mode of actionsimilar to or identical to a drug from Table 3 to Table 7). The resultsmay be referred to herein as a “report”. The report may include otherinformation based on assaying the SNPs disclosed herein, alone or incombination with other SNPs, and/or an individual's allele/genotype atthe SNPs disclosed herein, alone or in combination with other SNPs,etc.), and/or any other information pertaining to a test.

A tangible report can optionally be generated as part of a testingprocess (which may be interchangeably referred to herein as “reporting”,or as “providing” a report, “producing” a report, or “generating” areport).

Examples of tangible reports may include, but are not limited to,reports in paper (such as computer-generated printouts of test resultsor hand written reports) or equivalent formats and reports stored oncomputer readable medium (such as a CD, USB flash drive or otherremovable storage device, computer hard drive, or computer networkserver, etc.). Reports, particularly those stored on computer readablemedium, can be part of a database, which may optionally be accessiblevia the internet (such as a database of patient records or geneticinformation stored on a computer network server, which may be a “securedatabase” that has security features that limit access to the report,such as to allow only the patient and the patient's medicalpractitioners to view the report while preventing other unauthorizedindividuals from viewing the report, for example). In addition to, or asan alternative to, generating a tangible report, reports can also bedisplayed on a computer screen (or the display of another electronicdevice or instrument).

In addition to, or as an alternative to, the report may be “intangible”in that it is orally presented to another.

A tangible report may be hand written or may be prepared using acomputer.

A report may be provided to the individual who can then implement theinformation and/or instructions contained therein.

A report may be provided to a health care professional who can thenimplement the information and/or instructions contained therein and/orinstruct the individual (e.g., prescribe and make a recommendation).

A report can include, for example, an individual's predicted drugresponsiveness (e.g., to a drug disclosed in Table 3 to Table 7 and/oran alternate drug having a mode of action similar to or identical to adrug from Table 3 to Table 7 based upon his/her composite IL-1 genotypeor IL-1 genotype pattern, as disclosed in Table 1 and Table 2 and statusof one or more clinical indicators, as disclosed herein; theallele/genotype that an individual carries at the SNP locationsdisclosed herein; the status of his/her clinical indicators; and/orhis/her composite IL-1 genotype or IL-1 genotype pattern. Thus, forexample, the report can include information of medical/biologicalsignificance (e.g., drug responsiveness, suggested treatment, andprophylactic methods). The report may just include allele/genotypeinformation and/or a composite IL-1 genotype or IL-1 genotype patternand status of one or more clinical indicators but without includingdisease risk or other medical/biological significance; thus, theindividual viewing the report can use the allele/genotype informationand/or composite IL-1 genotype or IL-1 genotype pattern and status ofone or more clinical indicators to determine the associated disease riskor other medical/biological significance from a source outside of thereport itself, such as from a medical practitioner, publication,website, etc., which may optionally be linked to the report such as by ahyperlink.

A report can further be “transmitted” or “communicated” (these terms maybe used herein interchangeably), such as to the individual who wastested, a medical practitioner (e.g., a doctor, nurse, clinicallaboratory practitioner, genetic counselor, etc.), a healthcareorganization, a clinical laboratory, and/or any other party or requesterintended to view or possess the report. The act of “transmitting” or“communicating” a report can be by any means known in the art, based onthe format of the report. Furthermore, “transmitting” or “communicating”a report can include delivering a report (“pushing”) and/or retrieving(“pulling”) a report. For example, reports can betransmitted/communicated by various means, including being physicallytransferred between parties (such as for reports in paper format) suchas by being physically delivered from one party to another, or by beingtransmitted electronically or in signal form (e.g., via e-mail or overthe internet, by facsimile, and/or by any wired or wirelesscommunication methods known in the art) such as by being retrieved froma database stored on a computer network server.

Additional teaching relevant to the present invention are described inone or more of the following: U.S. Pat. Nos. 5,686,246, 5,698,399,5,808,918, 6,108,635, 6,140,047, 6,210,877, 6,251,598, 6,268,142,6,383,775, 6,437,216, 6,524,795, 6,551,785, 6,558,905, 6,706,478,6,713,253, 6,720,141, 6,730,476, 6,733,967, 6,746,839, 7,723,028,7,820,383, 8,101,360, 8,105,775, US 2002/0182612, US 2003/0100031, US2003/0124524, US 2003/0152947, US 2003/0235890, US 2004/0152124, US2005/0032077, US 2005/0064453, US 2005/0171338, US 2005/0282198, US2006/0183161, US 2006/0252050, US 2007/0264645, US 2007/0275104, US2008/0118920, US 2008/0187920, US 2008/0199865, US 2008/0254476, US2008/0254477, US 2008/0254478, US 2008/0311581, US 2009/0023147, US2009/0093396, US 2009/0163460, US 2009/0170105, US 2009/0191564, US2010/0028893, US 2010/0129798, US 2010/0255475, US 2010/0279280, US2011/0008906, US 2013/0011841, US 2003/0175764, US 2004/0110168, US2010/0098775, US 2010/0098809, US 2010/0105038, US 2010/0112570, US2010/0136561, US 2012/0208187, US 2013/0337448, and U.S. 62/277,760,each of which is incorporated herein by reference in their entireties.

Definitions

The term “single nucleotide polymorphisms” (SNPs) refers to a variationin the sequence of a gene in the genome of a population that arises asthe result of a single base change, such as an insertion, deletion or, achange in a single base. A locus is the site at which divergence occurs.SNPs can result in modified amino acid sequences, altering structure andfunction of coded protein, and influence the splicing process whenpresent at exon-intron transitions and modify gene transcription whenpart of promoters. This modification can lead to altered levels ofprotein expression.

As used herein the term subject is meant to include any human subject. Asubject may be less than 60 years old. The subject may have had one, to,three or more cardiac events.

As used herein, the terms “treat,” treating,” “treatment,” and the likerefer to reducing or ameliorating a disorder and/or a symptom associatedtherewith. It will be appreciated that, although not precluded, treatinga disorder or condition does not require that the disorder, condition orsymptoms associated therewith be completely eliminated. Treating mayinclude a health care professional or diagnostic scientist making arecommendation to a subject for a desired course of action or treatmentregimen, e.g., a prescription.

As used herein, the terms “prevent,” “preventing,” “prevention,”“prophylactic treatment” and the like refer to reducing the probabilityof developing a disorder or condition in a subject, who does not have,but is at risk of or susceptible to developing a disorder or condition.

As used herein, the terms “drug”, “medication”, “therapeutic”, “activeagent”, “therapeutic compound”, “composition”, or “compound” are usedinterchangeably and refer to any chemical entity, pharmaceutical, drug,biological, botanical, and the like that can be used to treat or preventa disease, illness, condition, or disorder of bodily function. A drugmay comprise both known and potentially therapeutic compounds. A drugmay be determined to be therapeutic by screening using the screeningknown to those having ordinary skill in the art. A “known therapeuticcompound”, “drug”, or “medication” refers to a therapeutic compound thathas been shown (e.g., through animal trials or prior experience withadministration to humans) to be effective in such treatment. A“therapeutic regimen” relates to a treatment comprising a “drug”,“medication”, “therapeutic”, “active agent”, “therapeutic compound”,“composition”, or “compound” as disclosed herein and/or a treatmentcomprising behavioral modification by the subject and/or a treatmentcomprising a surgical means.

Although methods and materials similar or equivalent to those describedherein can be used in the practice or testing of the present invention,suitable methods and materials are described below. All publications,patent applications, patents, and other references mentioned herein areincorporated by reference in their entirety. The references cited hereinare not admitted to be prior art to the claimed invention. In the caseof conflict, the present Specification, including definitions, willcontrol. In addition, the materials, methods, and examples areillustrative only and are not intended to be limiting.

As used in this Specification and the appended claims, the singularforms “a,” “an” and “the” include plural referents unless the contextclearly dictates otherwise.

Unless specifically stated or obvious from context, as used herein, theterm “or” is understood to be inclusive and covers both “or” and “and”.

The terms “one or more”, “at least one”, “more than one”, and the likeare understood to include but not be limited to at least 1, 2, 3, 4, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42,43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60,61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96,97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111,112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125,126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139,140, 141, 142, 143, 144, 145, 146, 147, 148, 149 or 150, 200, 300, 400,500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000 or more and anynumber in between.

Conversely, the term “no more than” includes each value less than thestated value. For example, “no more than 100 nucleotides” includes 100,99, 98, 97, 96, 95, 94, 93, 92, 91, 90, 89, 88, 87, 86, 85, 84, 83, 82,81, 80, 79, 78, 77, 76, 75, 74, 73, 72, 71, 70, 69, 68, 67, 66, 65, 64,63, 62, 61, 60, 59, 58, 57, 56, 55, 54, 53, 52, 51, 50, 49, 48, 47, 46,45, 44, 43, 42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28,27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10,9, 8, 7, 6, 5, 4, 3, 2, 1, and 0 nucleotides.

The terms “plurality”, “at least two”, “two or more”, “at least second”,and the like, are understood to include but not limited to at least 2,3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58,59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109,110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123,124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137,138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149 or 150, 200,300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000 or moreand any number in between.

Throughout the specification the word “comprising,” or variations suchas “comprises” or “comprising,” will be understood to imply theinclusion of a stated element, integer or step, or group of elements,integers or steps, but not the exclusion of any other element, integeror step, or group of elements, integers or steps.

Unless specifically stated or obvious from context, as used herein, theterm “about” is understood as within a range of normal tolerance in theart, for example within 2 standard deviations of the mean. About can beunderstood as within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%,0.1%, 0.05%, 0.01%, or 0.001% of the stated value. Unless otherwiseclear from the context, all numerical values provided herein aremodified by the term “about”.

Although methods and materials similar or equivalent to those describedherein can be used in the practice or testing of the present invention,suitable methods and materials are described below. All publications,patent applications, patents, and other references mentioned herein areincorporated by reference in their entirety. The references cited hereinare not admitted to be prior art to the claimed invention. In the caseof conflict, the present Specification, including definitions, willcontrol. In addition, the materials, methods, and examples areillustrative only and are not intended to be limiting.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this application belongs and as commonly used in theart to which this application belongs; such art is incorporated byreference in its entirety.

Any of the above aspects and embodiments can be combined with any otheraspect or embodiment as disclosed in the Summary, Drawings, and/or inthe Detailed Description sections, including the belowexamples/embodiments.

Example 1 General Methods

Study Population

This study enrolled 603 consecutive patients undergoing a diagnosticcoronary angiography based on clinical suspicion of coronary arterydisease at the 2^(nd) Department of Cardiology in the UniversityHospital of Ioannina and the Catheterization Laboratory of 1st IKAHospital in Athens, from January 2010 to December 2012. Patients werebetween 18 years to 90 years at entry (index coronary angiography) andof both genders. Patients with a history of any coronaryrevascularization procedure, severe valvular disease, congenital heartdisease, cardiomyopathies as well as those on hemodialysis wereexcluded. Additionally, patients with diabetes mellitus were excluded tobe able to compare to prior studies^(1,2) where such patients wereexcluded, since they are very high risk group that may mask otherunderlying relationships.

Study Design

The study was prospectively designed to test the association of CAD withpro-inflammatory and pro-thrombotic biomarkers in relation to thepresence of specific IL-1 genotype groups known to be associated withhigher inflammatory responses. The study protocol was approved by theEthics Committee at University Hospital of Ioannina. The study compliedwith the Declaration of Helsinki and all participants provided writteninformed consent.

Parameters recorded in the study were derived from patient's medicalhistory, physical examination, laboratory evaluations, and coronaryangiography. All subjects underwent catheterization and coronaryangiography according to the standard Judkins technique. Angiograms wereassessed in multiple projections independently by two experiencedoperators and a consensus was reached. Angiographically significantdisease was defined as diameter stenosis >50% in any one majorepicardial coronary artery.

Blood samples were drawn after an overnight fast and just beforecoronary angiography for stable coronary syndromes. In patients withunstable coronary syndromes blood samples for determination of lipidslevels and fasting glucose were drawn either before coronary angiographyor the next morning depending on the presence of fasting state.

Of the 603 patients enrolled, 512 patients (85%) were contacted by afollow-up by telephone between May and July 2015 [median follow-up of 45months (interquartile range, 24-60 months)]. The remaining 91 patientseither refused to participate in the follow-up or could not becontacted. Of the 512 patients with available follow-up, 52 (10%) hadone or more events categorized as cardiovascular death, acute coronarysyndrome, new revascularization unrelated to the original angiography,stroke, or death of any cause. The follow-up events of these patientsconsisted of 22 deaths (17 cardiac), 16 myocardial infarctions, 8coronary revascularizations, and 20 strokes.

Genetic Analysis

Single nucleotide polymorphisms (SNPs) were genotyped at two loci in theIL-1β gene (rs16944 and rs1143634) and one in the IL-1a gene (rs17561),as previously described.^(1,2) Briefly, extracted DNA from theparticipants was sent to Interleukin Genetics, Inc. (Waltham, Mass.),and genotyped at their CLIA certified genotyping laboratory. Multiplexedpolymerase chain reactions (PCR) specifically targeting surroundingsequences for each of the SNPs were treated with exonuclease I andshrimp alkaline phosphatase (USB). Primer extension reactions andgenotype detection was performed using an automated genotyping system[Genome Lab SNPStream (Beckman-Coulter)]. Allele calls were determinedby the SNPstream software and verified by a laboratory technologist.

IL-1 Composite Genotype Patterns

IL-1 composite genotype patterns (Positive-IL1(+) and Negative (IL1(−))are identical to those used in Tsimikas, et al.² and include the singlenucleotide polymorphisms: rs 17561 (G>T), rs1143634 (C>T), and rs16944(C>T).

Biomarker Analysis

Total cholesterol, HDL cholesterol (HDL-C) and triglycerides weremeasured with commercially available kits. LDL cholesterol (LDL-C) wasestimated using the Friedewald formula. Serum hsCRP was measured usingrate turbidimetry (IMMAGE Immunochemistry Systems and Calibrator 5 Plus,Beckman Coulter Inc, Fullerton, Calif., USA).

OxPL-apoB levels were measured in a chemiluminescent immunoassay usingthe murine monoclonal antibody E06 that recognizes the phosphocholinegroup on oxidized but not on native phospholipids (details in Byun et aland references therein) and results reported in nanomoles/liter (nM).The OxPL-apoB measure reflects OxPL on all apoB-100-containinglipoproteins, but we have shown previously that it primarily reflectsthe biological activity and clinical risk of Lp(a), which is the majorlipoprotein carrier of OxPL in plasma, and which carries ˜85% of OxPL onapoB-100 containing lipoproteins. Lp(a) levels were determined with asandwich ELISA as previously described.⁴

Statistical Analysis

For genetic data analysis, standard data quality checks includinggenotype call rate, percentage of missing genotypes, minor allelefrequencies, and tests of HWE were carried out.

Logistic regression was used to determine odds ratios (OR) for CAD ofeach quartile of OxPL-apoB and Lp(a) relative to the lowest quartile.Trend tests were done by repeating analyses with quartiles codednumerically. Analyses were done for all patients and with stratificationfor IL-1 genotype and age ≤60.

Multivariate logistic analysis was used to adjust for factors known tomodify risk for CAD including sex, current smoking, hypertension,triglycerides (per doubling), LDL cholesterol (per increase of 25mg/dl), HDL cholesterol (per increase of 25 mg/dl) and experimentalfactors of hsCRP (per doubling), OxPL/apoB (per doubling), Lp(a) (perdoubling), and presence of IL-1+ genotype. Formal testing forstatistical interaction of IL-1 genotype with OXPL/apoB and 1p(a) on CADrisk was carried out by adding an interaction term to the logisticregression model. Event-free survival curves were constructed by the Coxregression proportional hazard regression method. Multivariable analysiswas used to adjust for gender, current smoking, hypertension,triglycerides (per doubling), LDL cholesterol (per increase of 25mg/dl), HDL cholesterol (per increase of 25 mg/dl) and hsCRP (perdoubling). Events were defined as CVD death, non-fatal MI, newrevascularization and stroke/TIA subsequent to enrollment during thefollow-up period.

Example 2: Baseline Characteristics of the Study Group

The baseline characteristics of the 603 patients, separated by IL1status, are presented in Table 8. The total cohort had a mean age of63±11 and was 71% male. 390 patients (65%) were IL-1(+), typical ofprior data in Caucasian populations. Cardiovascular risk factors wereprevalent and included current smoking (41%), hypertension (73%),hypercholesterolemia (78%), and family history of CAD (33%). Thebaseline use of anti-platelet agents and statins was 31% and 42%,respectively. The indication for angiography was acute coronary syndromein 19% and suspected CAD in 81% of patients. Mean LDL-C was 126±40mg/dL, median (IQR) Lp(a) was 9.2 (4.4, 20.9) mg/dl and median (IQR)OxPL-apoB was 12.5 (8.1, 14.0). The baseline characteristics were notsignificantly different between IL1(+) and IL1(−) groups, except forfamily history, total cholesterol and LDL-C being higher in the IL1(−)group. Also, the baseline characteristics were similar between patientswith and without follow-up data.

The Spearman correlation of Lp(a) levels to OxPL-apoB levels in theentire group was R=0.469, p<0.001 (FIG. 5), and R=0.467, p<0.001 inIL1(+) and R=0.473, p<0.001 in IL1(−) patients. Lp(a) and OxPL-apoB weresignificantly but weakly correlated only with the presence of a familyhistory of CAD (R=0.086, p=0.034 and R=0.135, p=0.001 respectively).

Example 3: Relationship of Lp(a) and OxPL-apoB and forAngiographically-Determined CAD

The number (%) of patients with no CAD was 265(44%), and non-significantCAD was 51 (9%). Among the 287 (47%) with CAD, the distribution of1-vessel, 2-vessels and 3-vessels were as follows: 316(53%), 183(30%),84 (14%) and 20 (3%), respectively.

Analysis by Lp(a) quartiles revealed a linear, significant relationshipbetween increasing levels of Lp(a) and OR for angiographicallydetermined CAD in IL1(+) patients ≤60 years old, reaching an OR (95% CI)of 2.90 (1.07-7.86) (p=0.036) for quartile 4 versus quartile 1 (Table9). In contrast, no significant differences were noted in IL1(−)patients or in patients >60 years old.

Analysis by OxPL-apoB quartiles revealed similar trends, but withborderline non-significance, for angiographically determined CAD inIL1(+) patients ≤60 years of age, reaching an OR (95% CI) of 2.29(0.72-7.31) (p=0.056 for quartile 4 versus quartile 1 (Table 10).

In patients ≤60 years old, a multivariable-adjusted logistic regressionanalysis was performed assessing angiographically-determined CAD, whichincluded sex, current smoking, hypertension, HDL-C per 10 mg/dLincrease, LDL-C per 25 mg/dL increase, triglycerides per doubling, hsCRPper doubling and Lp(a) per doubling. In this model, a doubling of Lp(a)was the only significant predictor of CAD with an OR (95% CI) of 1.36(1.05-1.76), p=0.019 (FIG. 6A). Performing a similar multivariableanalysis but substituting a doubling of OxPL-apoB for Lp(a) showed an OR(95% CI) of 1.64 (0.86-3.13), p=0.136 (FIG. 6B).

Example 4: Event-Free Survival During Median 45 Month Follow Up

Hazard ratios were determined with multivariable-adjusted Coxproportional hazard analysis by evaluating above or below the median(9.2 mg/dL) Lp(a) according to IL1 genotype status (4 groups: IL1(+)patients with above median Lp(a), IL1(+) patients with below medianLp(a), IL1(−) patients with above median Lp(a) and IL1(−) patients withbelow median Lp(a)). Co-variates included age, gender, active smoking,hypertension, HDL-C, LDL-C, triglycerides and hsCRP. There were 46 MACEevents, defined as CVD death, non-fatal MI, stroke andrevascularization. Significant differences in time to MACE were presentamong the 4 groups, with the worse event-free cumulative survivalpresent in the IL1(+) subjects with above median Lp(a), with a HR (95%CI) of 3.59 (1.07-12.03) (p=0.039) compared to IL1(−) subjects withbelow median Lp(a).

Additional analysis comparing IL1(+) subjects with above median Lp(a)against the other 3 groups showed a HR (95% CI) of 2.29 (1.27, 4.13),p=0.006 (FIG. 7). Removing the 8 cases of revascularization from theMACE endpoint increased the HR (95% CI) for in the IL1(+) subjects withabove median Lp(a) versus IL1(−) subjects with below median Lp(a) to10.86 (1.46-81.05) (p=0.020). The OR (95% CI) was 3.10 (1.61, 5.97),p=0.001 versus the other 3 groups. Adding OxPL-apoB to the multivariablemodel resulted in persistence of significance for IL1(+) patients withabove median Lp(a), with a HR OR (95% CI) at 3.78 (1.10-13.01) (p=0.035)compared to IL1(−) subjects with below median Lp(a). Similar resultswere present for the other analyses as above when adding OxPL-apoB tothe models (data not shown). Interactions of quartiles of Lp(a) with IL1genotype status were significant in patients <60 years old (p=0.046).

Evaluating OxPL-apoB in the multivariable model without Lp(a) showed anOR (95% CI) for Q4 vs Q1 of 2.42 (0.71-8.28) (p=0.160).

Example 5: Relationship of Lp(a), IL1 Genotypes and HsCRP

hsCRP levels did not differ significantly between IL1(+) and IL1(−)patients. Lp(a) was positively yet weakly correlated with hsCRP(R=0.096, p=0.020). In the overall group, hsCRP was an independentpredictor of CAD in both IL1(+) (OR (95% CI) of 1.19, P=0.003) andIL1(−) (OR of 1.54, P<0.001) patients; a similar effect was shown inIL1(+) patients ≤60 years old. The OR (95% CI) for the Lp(a) associationwith CAD in IL1(+) patients with hsCRP >2.82 mg/L (median value) was2.80, p=0.038 for quartile IV vs quartile I, and in those with hsCRP<2.82 mg/L, the OR was 1.59, p=0.289 for quartile IV vs quartile I.Removing the 69 patients with recent acute coronary syndrome yieldedsimilar results, with OR (95% CI) of 3.02, p=0.046 for the Lp(a)association with CAD in IL1(+) patients with hsCRP above the median(quartile IV vs quartile I), and OR (95% CI) 1.34, p=0.544 in thosebelow the median.

TABLE 8 Baseline characteristics in the entire population and by IL-1genotype status All patients IL-1(+) patients IL-1(−) patients P value(n = 603) (n = 390) (n = 213) (IL1(+) vs IL1(−) Age, years 63 ± 11 64 ±11 62 ± 10 0.079 Males, n (%) 430 (71) 275 (71) 155 (73) 0.573 CurrentSmokers, n (%) 249 (41) 164 (42) 85 (40) 0.665 Hypertension, n (%) 438(73) 286 (73) 152 (71) 0.633 Hypercholesterolemia, n (%) 473 (78) 303(78) 170 (80) 0.605 Family history of CAD, n (%) 198 (33) 116 (30) 82(39) 0.030 Medications, n (%) Antiplatelet agents 185 (31) 123 (32) 62(29) 0.580 Statins 252 (42) 169 (43) 83 (39) 0.342 Beta blockers 180(30) 115 (30) 65 (31) 0.852 RAAS inhibitors 215 (36) 133 (34) 82 (39)0.287 Calcium channel blockers 157 (26) 109 (28) 48 (23) 0.174 Diuretics134 (22) 92 (24) 42 (20) 0.306 History of CAD, n (%) 106 (18) 64 (16) 42(20) 0.315 Indication for angiography Acute coronary syndrome 114 (19)69 (18) 45 (21) 0.317 Suspected stable CAD 489 (81) 321 (82) 168 (79)0.765 Systolic BP, mmHg 134 ± 21  133 ± 21  135 ± 19  0.206 DiastolicBP, mmHg 79 ± 12 79 ± 13 80 ± 12 0.476 Body mass index, kg/m² 27.8 ±3.7  27.8 ± 3.8  28.0 ± 3.6  0.556 Fasting glucose, mg/dl 99 (91, 109)99 (91, 108) 99 (91, 110) 0.733 MDRD-GFR, ml/min/1.73 m² 73.9 ± 16.573.2 ± 17.0 75.2 ± 15.6 0.160 Total cholesterol, mg/dl 195 ± 43  192 ±43  199 ± 43  0.047 HDL cholesterol, mg/dl 43 ± 16 42 ± 16 43 ± 17 0.765LDL cholesterol, mg/dl 126 ± 40  123 ± 40  130 ± 40  0.035Triglycerides, mg/dl 117 (92, 164) 118 (92, 169) 112 (91, 156) 0.570Hs-CRP, mg/L 2.8 (1.16, 6.9) 2.7 (1.1, 6.8) 3.2 (1.0, 7.5) 0.477 Lp(a),mg/dl 9.2 (4.4, 20.9) 8.8 (4.3, 20.4) 10.2 (4.6, 21.5) 0.428 OxPL-apoB,nM 12.5 (8.1, 14.0) 12.5 (8.29, 14.7) 12.6 (7.8, 14.9) 0.942 Presence ofCAD, n (%) No CAD 265 (44) 172 (44) 93 (44) 0.974 Non-significant CAD(<50% stenosis) 51 (9) 33 (9) 18 (8) 0.965 Any 287 (47) 185 (47) 102(48) 0.848 1-vessel 183 (30) 115 (30) 68 (32) 0.540 2-vessel 84 (14) 59(15) 25 (12) 0.314 3-vessel 20 (3) 11 (3) 9 (4) 0.348 Abbreviations:IL-1, interleukin1; CAD, coronary artery disease; BP, blood pressure;MDRD-GFR, Modification of Diet in Renal Disease study - Glomerularfiltration rate; HDL, high density lipoprotein; LDL, Low densitylipoprotein; hsCRP, high sensitivity C-reactive protein; Lp(a),lipoprotein a; OxPL-apoB, oxidized phospholipids on apolipoprotein B.

TABLE 9 Odds ratios for angiographically-determined CAD (>50% diameterstenosis) in patients ≤60 and >60 years old according to quartiles forLp(a), and IL-1 genotype. IL-1(+) IL-1(−) Total No. No. with CAD (%) OR(95% CI) Total No. No. with CAD (%) OR (95% CI) Age ≤60 yr Quartile I 40 9 (23) 1.00 26 11 (42) 1.00 Quartile II 35 12 (34) 1.78 (0.65-4.98) 1710 (59) 1.95 (0.56-6.73) Quartile III 29 11 (38) 2.11 (0.73-6.05) 25 10(40) 0.91 (0.30-2.78) Quartile IV 35 16 (46) 2.90 (1.07-7.86) 28 15 (54)1.57 (0.54-4.61) OR (95% CI) 1.39 (1.02-1.90) 1.08 (0.77-1.53) perquartile P for trend  0.036  0.644 Age >60 yr Quartile I 58 30 (52) 1.0026 10 (39) 1.00 Quartile II 68 36 (53) 1.05 (0.52-2.12) 31 14 (45) 1.32(0.46-3.81) Quartile III 66 35 (53) 1.05 (0.52-2.14) 31 14 (45) 1.32(0.46-3.81) Quartile IV 59 36 (61) 1.46 (0.70-3.04) 29 18 (62) 2.62(0.88-7.78) OR (95% CI) 1.21 (0.95-1.53) 1.33 (0.95-1.87) for quartile Pfor trend  0.130  0.097 Abbreviations: CAD, coronary artery disease;Lp(a), lipoprotein(a); IL-1, interleukin 1; OR, odds ratio. Quartile ILp(a) <4.40 mg/dL, Quartile II Lp(a) 4.40-9.10 mg/dL, Quartile III Lp(a)9.15-20.9 mg/dL and Quartile IV Lp(a) >20.9 mg/dL.

TABLE 10 Odds ratios for angiographically-determined CAD (>50% diameterstenosis) in patients ≤60 and ≥60 years old according to quartiles forOxPL-apoB and IL-1 genotype. IL-1(+) IL-1(−) Total No. No. with CAD (%)OR (95% CI) Total No. No. with CAD (%) OR (95% CI) Age ≤60 yr Quartile I25  6 (24) 1.00 31 18 (58) 1.00 Quartile II 45 12 (45) 1.15 (0.37-3.57)22 10 (46) 0.60 (0.20-1.81) Quartile III 38 17 (45) 2.56 (0.84-7.85) 18 8 (44) 0.58 (0.18-1.87) Quartile IV 31 13 (42) 2.29 (0.72-7.31) 25 10(40) 0.48 (0.17-1.41) OR (95% CI) 1.41 (0.99-2.00) 0.79 (0.56-1.12) perquartile P for trend  0.056  0.185 Age >60 yr Quartile I 65 39 (60) 1.0026 15 (58) 1.00 Quartile II 59 30 (51) 0.69 (0.34-1.41) 27 12 (44) 0.59(0.20-1.74) Quartile III 59 31 (53) 0.74 (0.36-1.51) 28 11 (39) 0.48(0.16-1.41) Quartile IV 58 37 (54) 0.80 (0.40-1.58) 36 18 (50) 0.73(0.27-2.03) OR (95% CI) 0.94 (0.76-1.17) 0.91 (0.66-1.26) per quartile Pfor trend  0.583  0.578 Abbreviations: CAD, coronary artery disease;OxPL/apoB, oxidized phospholipids on apolipoprotein B; IL-1, interleukin1; OR, odds ratio. Quartile I OxPL-apoB <8.0 nmol/L, Quartile IIOxPL-apoB 8.0-12.5 nmol/L, Quartile III OxPL-apoB 12.51-14.7 nmol/L andQuartile IV OxPL-apoB >14.7 nmol/L.

REFERENCES

-   Chen, H., et al., “Single Nucleotide Polymorphisms in the Human    Interleukin-1B Gene Affect Transcription According to Haplotype    Context.” Human Molecular Genetics (2006), 15.4: 519-529.-   Libby, P., “History of Discovery: Inflammation in Atherosclerosis.”    Arterioscler Thromb Vasc Biol. (2012) 32(9): 2045-2015.-   Ray, K K., “Interleukin-1 Revisited: Further Insights Into Its Role    in Atherosclerosis and as a Potential Therapeutic Target for    Treatment.” Journal of the American College of Cardiology (2014),    63.17: 1735-1738-   Ridker, P. M. “Targeting inflammatory pathways for the treatment of    cardiovascular disease.” European Heart Journal (2014) 35.-   Rogus J., et al., “IL1B Gene Promoter Haplotype Pairs Predict    Clinical Levels of Interleukin-1β and C-reactive Protein.” Human    Genetics (2008). 123.4: 387-398.-   Ross, “Atherosclerosis—An inflammatory disease.” N Engl J Med    (1999); 340:115-126.-   Tsimikas S., et al., “Antisense oligonucleotides targeting    apolipoprotein(a) in people with raised lipoprotein(a): two    randomized, double-blind, placebo controlled, dose-ranging trials.”    The Lancet, Sep. 21, 2016.-   Tsimikas S., et al., “Oxidized Phospholipids, Lp(a) Lipoprotein, and    Coronary Artery Disease.” New England Journal of Medicine (2005),    353:46-57.-   Tsmikas S., et al., “Pro-Inflammatory Interleukin-1 Genotypes    Potentiate the risk of Coronary Artery Disease and Cardiovascular    Events Mediated by Oxidized Phospholipids and Lipoprotein(a).” J.    Am. College of Cardiology (2014). Vol. 63, No. 17.-   Yusuf et al., “Effect of potentially modifiable risk factors    associated with myocardial infarction in 52 countries (the    INTERHEART study): case-control study.” Lancet, 364:937-52 (2004).

Other Embodiments

While the invention has been described in conjunction with the detaileddescription thereof, the foregoing description is intended to illustrateand not limit the scope of the invention, which is defined by the scopeof the appended claims. Other aspects, advantages, and modifications arewithin the scope of the following claims.

What is claimed is:
 1. A method for reducing the risk of a cardiac eventin a human subject comprising: (a) obtaining information regarding thehuman subject's single nucleotide polymorphism (SNP) alleles for each ofthe rs16944 polymorphic locus, the rs1143623 polymorphic locus, thers4848306 polymorphic locus, the rs17561 polymorphic locus, and thers1143634 polymorphic locus; (b) determining that the subject has apositive IL-1 genotype pattern when the IL-1 genotype pattern obtainedin step (a) matches an IL-1 genotype pattern that is selected from thegroup consisting of: (i) T/T or T/G at rs17561, C/C, T/T, C/T or T/C atrs4848306, G/G at rs1143623, C/C at rs16944 and T/T or T/C at rs1143634;(ii) G/G at rs17561, C/C, T/T, C/T or T/C at rs4848306, G/G atrs1143623, C/C at rs16944 and C/C, T/T, C/T or T/C at rs1143634; (iii)G/G, T/T, G/T or T/G at rs17561, C/C, T/T, C/T or T/C at rs4848306, G/Gat rs1143623, C/C at rs16944 and C/C at rs1143634; (iv) T/T or T/G atrs17561, C/C or C/T at rs4848306, G/G at rs1143623, C/T at rs16944 andT/T or T/C at rs1143634; (v) G/G at rs17561, C/C or C/T at rs4848306,G/G at rs1143623, C/T at rs16944 and C/C, T/T, C/T or T/C at rs1143634;(vi) G/G, T/T, G/T or T/G at rs17561, C/C or C/T at rs4848306, G/G atrs1143623, C/T at rs16944 and C/C at rs1143634; (vii) T/T or T/G atrs17561, C/C at rs4848306, C/G at rs1143623, C/T at rs16944 and T/T orT/C at rs1143634; (viii) G/G at rs17561, C/C at rs4848306, C/G atrs1143623, C/T at rs16944 and C/C, T/T, C/T or T/C at rs1143634; (ix)G/G, T/T, G/T or T/G at rs17561, C/C at rs4848306, C/G at rs1143623, C/Tat rs16944 and C/C at rs1143634; (x) T/T or T/G at rs17561, C/C atrs4848306, G/G at rs1143623, T/T at rs16944 and T/T or T/C at rs1143634;(xi) G/G at rs17561, C/C at rs4848306, G/G at rs1143623, T/T at rs16944and C/C, T/T, C/T or T/C at rs1143634; and (xii) G/G, T/T, G/T or T/G atrs17561, C/C at rs4848306, G/G at rs1143623, T/T at rs16944 and C/C atrs1143634; (c) determining the plasma concentration of LDL-C and/orLp(a) in a plasma sample obtained from the subject; (d) diagnosing thesubject as at risk of a cardiac event when the subject has a positiveIL-1 pattern and (i) a total LDL-C plasma concentration of at least 50mg/dL, and/or (ii) a total Lp(a) plasma concentration of at least 5mg/dL; and (e) administering an anti-cholesterol drug that lowers thelevel of LDL-C or Lp(a) to the subject.
 2. The method of claim 1,wherein the Lp(a) reducing drug is APO(a)L_(RX), Alirocumab or ARC-LPA.3. A method for determining whether a human subject would receive atherapeutic benefit from an anti-cholesterol drug that reduces a levelof LDL-C or Lp(a), comprising steps of: (a) selecting a human subjectwith a diagnosis of, suspected of having, or at risk for elevated IL 1β;(b) obtaining information regarding the human subject's singlenucleotide polymorphism (SNP) alleles for each of the rs16944polymorphic locus, the rs1143623 polymorphic locus, the rs4848306polymorphic locus, the rs17561 polymorphic locus, and the rs1143634polymorphic locus; (c) determining that the human subject has a positiveIL-1 genotype pattern when the IL-1 genotype pattern obtained in (c)matches an IL-1 genotype pattern selected from the group consisting of:(i) T/T or T/G at rs17561, C/C, T/T, C/T or T/C at rs4848306, G/G atrs1143623, C/C at rs16944 and T/T or T/C at rs1143634; (ii) G/G atrs17561, C/C, T/T, C/T or T/C at rs4848306, G/G at rs1143623, C/C atrs16944 and C/C, T/T, C/T or T/C at rs1143634; (iii) G/G, T/T, G/T orT/G at rs17561, C/C, T/T, C/T or T/C at rs4848306, G/G at rs1143623, C/Cat rs16944 and C/C at rs1143634; (iv) T/T or T/G at rs17561, C/C or C/Tat rs4848306, G/G at rs1143623, C/T at rs16944 and T/T or T/C atrs1143634; (v) G/G at rs17561, C/C or C/T at rs4848306, G/G atrs1143623, C/T at rs16944 and C/C, T/T, C/T or T/C at rs1143634; (vi)G/G, T/T, G/T or T/G at rs17561, C/C or C/T at rs4848306, G/G atrs1143623, C/T at rs16944 and C/C at rs1143634; (vii) T/T or T/G atrs17561, C/C at rs4848306, C/G at rs1143623, C/T at rs16944 and T/T orT/C at rs1143634; (viii) G/G at rs17561, C/C at rs4848306, C/G atrs1143623, C/T at rs16944 and C/C, T/T, C/T or T/C at rs1143634; (ix)G/G, T/T, G/T or T/G at rs17561, C/C at rs4848306, C/G at rs1143623, C/Tat rs16944 and C/C at rs1143634; (x) T/T or T/G at rs17561, C/C atrs4848306, G/G at rs1143623, T/T at rs16944 and T/T or T/C at rs1143634;(xi) G/G at rs17561, C/C at rs4848306, G/G at rs1143623, T/T at rs16944and C/C, T/T, C/T or T/C at rs1143634; and (xii) G/G, T/T, G/T or T/G atrs17561, C/C at rs4848306, G/G at rs1143623, T/T at rs16944 and C/C atrs1143634; (d) diagnosing the human subject as having elevated IL-1βwhen the human subject has a positive IL-1 genotype pattern determinedin step (c); and (e) administering an anti-cholesterol drug that reducesa level of LDL-C or Lp(a) to the human subject diagnosed in step (d). 4.The method of claim 1, wherein the anti-cholesterol drug that reducesthe level of LDL-C comprises a statin.
 5. The method of claim 1, whereinthe anti-cholesterol drug that reduces the level of Lp(a) comprises aPCSK9 inhibitor.
 6. The method of claim 5, wherein the PCSK9 inhibitorcomprises evolocumab or alirocumab.
 7. The method of claim 1, whereinthe anti-cholesterol drug that reduces the level of Lp(a) comprisesAPO(a)-L_(RX) or ARC-LPA.
 8. The method of claim 4, wherein the statincomprises lovastatin, amlodipine-atorvastatin, atorvastatin,rosuvastatin, evolocumab, ezetimibe-simvastatin, fluvastatin,fluvastatin, pitavastatin, niacin-lovastatin, niacin-simvastatin,prevastatin, or simvastatin.
 9. The method of claim 3, wherein theanti-cholesterol drug that reduces the level of Lp(a) comprises a PCSK9inhibitor.
 10. The method of claim 9, wherein the PCSK9 inhibitorcomprises evolocumab or alirocumab.
 11. The method of claim 3, whereinthe anti-cholesterol drug that reduces the level of Lp(a) comprisesAPO(a)-L_(RX) or ARC-LPA.
 12. The method of claim 3, wherein theanti-cholesterol drug that reduces the level of LDL-C comprises astatin.
 13. The method of claim 12, wherein the statin compriseslovastatin, amlodipine-atorvastatin, atorvastatin, rosuvastatin,evolocumab, ezetimibe-simvastatin, fluvastatin, fluvastatin,pitavastatin, niacin-lovastatin, niacin-simvastatin, prevastatin, orsimvastatin.